tag:blogger.com,1999:blog-262559832024-03-26T05:13:42.966+01:00Mining Drug Space"Communication is the essence of science" (Francis Crick)Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.comBlogger166125tag:blogger.com,1999:blog-26255983.post-19885711248590576662015-07-30T00:20:00.000+02:002017-05-30T18:27:41.374+02:00Data scientists - A view on decision making<div class="separator" style="clear: both; text-align: center;">
<i>"No, <a href="http://miningdrugs.blogspot.be/2012/12/cheminformatics-open-source-chemistry.html">'drug space' scientists</a> alone will not be able to handle exponential data growth"</i> </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqIYbVFnlvSpekt14nTYilzHIu6XA2cF2nb-VTA_m4tXSClHJOHat2Mu5SUCsidTBYzvPdH-TVLiynV78j4yBXEnwzE-SFI-wRubVMqdmAhxTux41mMizMLKjk7tUdtWWIDiFZ/s1600/moz-screenshot-3-729576.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="239" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqIYbVFnlvSpekt14nTYilzHIu6XA2cF2nb-VTA_m4tXSClHJOHat2Mu5SUCsidTBYzvPdH-TVLiynV78j4yBXEnwzE-SFI-wRubVMqdmAhxTux41mMizMLKjk7tUdtWWIDiFZ/s320/moz-screenshot-3-729576.png" width="320" /></a></div>
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source: <a href="http://www.anlytcs.com/2014/01/data-science-venn-diagram-v20.html">Steve's ML blog</a></div>
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<b>Why would people be interested in automating decisions via data science? </b></div>
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Clearly, I think this needs to happen to improve decision making, besides, I like unicorns as a fantasy fan ;-)</div>
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<b>Pros</b></div>
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<ul>
<li><b>Risk reduction</b></li>
<ul>
<li>data is growing exponential, but sense-making capacity is not. - <a href="http://miningdrugs.blogspot.com/2009/03/do-drug-innovation-while-information.html">do drug development (D3)</a></li>
<li>information overload requires some form of automated preprocessing - <a href="http://miningdrugs.blogspot.be/2009/01/collaboration-bullseye-20-information.html">collaboration bullseye</a></li>
<li>we need to enrich over a 'random decision making' - <a href="http://miningdrugs.blogspot.be/2006/10/bounded-rational-drug-design.html">bounded rational decision making</a></li>
</ul>
<li><b>Jobs </b>- there is a <a href="http://esa.gov/sites/default/files/the-importance-of-data-occupations-in-the-us-economy_0.pdf">20% higher employment rate</a> in the US in the data industry</li>
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<b>Cons</b></div>
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<ul>
<li><b>Personal </b>challenge - <a href="https://www.linkedin.com/pulse/20141202183759-103457178-data-scientist-owning-up-to-the-title">taking responsibility</a> in this domain means pretty much "learn as you go"<br /><i>"If we could put children in touch with their inner scientists, we might be able to bridge the divide between everyday knowledge and the apparently intimidating and elite apparatus of formal science"</i> [<a href="http://www.amacad.org/publications/winter2004/gopnik.pdf">finding our inner scientist</a>]</li>
<li><span style="text-align: justify;"><b>Change management and group dynamic</b> challenge - Top 10 reasons for not automating decisions:</span></li>
<ul>
<li><span style="text-align: justify;">1. <a href="http://www.ebizq.net/blogs/decision_management/2006/07/top_10_reasons_for_not_automat_9.php">You want my business users to do WHAT?</a></span></li>
<li><span style="text-align: justify;">2. <a href="http://www.ebizq.net/blogs/decision_management/2006/07/top_10_reasons_for_not_automat_8.php">Business users wouldn't know what to do with decision automation if they had it</a></span></li>
<li><span style="text-align: justify;">3. <a href="http://www.ebizq.net/blogs/decision_management/2006/07/top_10_reasons_for_not_automat_7.php">It will take too long to get results</a></span></li>
<li><span style="text-align: justify;">4. <a href="http://www.ebizq.net/blogs/decision_management/2006/07/top_10_reasons_for_not_automat_6.php">It will never work</a></span></li>
<li><span style="text-align: justify;">5. <a href="http://www.ebizq.net/blogs/decision_management/2006/07/top_10_reasons_for_not_automat_5.php">I can't afford it</a></span></li>
<li><span style="text-align: justify;">6. <a href="http://www.ebizq.net/blogs/decision_management/2006/06/top_10_reasons_for_not_automat_4.php">My new operational system will do that</a></span></li>
<li><span style="text-align: justify;">7. <a href="http://www.ebizq.net/blogs/decision_management/2006/06/top_10_reasons_for_not_automat_3.php">Why do I need more technology to handle business logic?</a></span></li>
<li><span style="text-align: justify;">8. <a href="http://www.ebizq.net/blogs/decision_management/2006/06/top_10_reasons_for_not_automat_2.php">We're doing fine as we are; why fix what isn't broken?</a></span></li>
<li><span style="text-align: justify;">9.<a href="http://www.ebizq.net/blogs/decision_management/2006/06/top_10_reasons_for_not_automat_1.php"> I would like to invest in business rules and decision management but my manager just doesn't get it</a></span></li>
<li><span style="text-align: justify;">10. <a href="http://www.ebizq.net/blogs/decision_management/2006/06/top_10_reasons_for_not_automat.php">We tried before and never got any results</a></span></li>
</ul>
<li>Lets not even go into technical, operational, and legal challenges, all of those are much easier to handle, since process driven.</li>
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Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.comtag:blogger.com,1999:blog-26255983.post-23934755223824998462012-12-29T21:46:00.002+01:002012-12-29T23:51:33.761+01:00Cheminformatics - Open source chemistry software and molecular databases broaden the research horizons of drug discovery<blockquote class="tr_bq">
"<i>Open source chemistry software and molecular databases broaden the research horizons of drug discovery</i>" [DOI <span style="color: black;"><a href="http://dx.doi.org/10.1145/2366316.2366334">10.1145/2366316.2366334</a></span>]</blockquote>
Here some additional thoughts for putting our <a href="http://dx.doi.org/10.1145/2366316.2366334">recent advocacy article and a call-for-action</a> for more collaboration between computer scientists and chem-informaticians into perspective. You surely might know that this article was a community effort triggered after the discussion on this blog article "<a href="http://blog.computationalcomplexity.org/2011/01/is-cheminformatics-new-bioinformatics.html">Is Cheminformatics the new Bioinformatics?</a>" (see also related historic content from <a href="http://blog.rguha.net/?p=913">Rajarshi</a> and <a href="http://nanoexplanations.wordpress.com/the-tcs-of-chemoinformatics/">Aaron</a>).<br />
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Three clarifications<br />
<h3>
<ul>
<li><span style="font-weight: normal;"><span style="font-size: small;">No, open source software is no "magic bullet", if not combined with community policies</span></span></li>
<li><span style="font-size: small; font-weight: normal;">No, "drug space" scientists alone will not be able to handle exponential data growth</span></li>
<li><span style="font-size: small; font-weight: normal;">Yes, I care about usability of data more than just the amount of it</span></li>
</ul>
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<span style="font-size: small;"><span style="font-weight: normal;"><br /></span></span></div>
</h3>
<h3>
No, open source software is no "magic bullet", if not combined with community policies</h3>
Please note that software can serve as amplifier and tool for reducing barriers, but not change the general "response to need" of people and even more so academic or business interests, which bounds personal interests, too.<br />
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In agreement to <a href="http://blog.rguha.net/?p=1026">Rajarshi</a> do I agree that the key aspect of software and standards is<br />
<blockquote class="tr_bq">
<i>It just needs somebody with the time and expertise to implement them. And the combination of these two (in the absence of funding) is not always easy to find.</i></blockquote>
Though, I must also be very clear -as said in the original post from <a href="http://pipeline.corante.com/archives/2012/04/12/a_federation_of_independent_researchers.php">Derek</a>- that community policies (<i>people collaboration</i>) will be at least as critical as software and standards (<i>information/tool collaboration</i>) for supporting a collaboration amplification. As said many times: <a href="http://miningdrugs.blogspot.be/2009/12/social-media-needs-to-support-different.html"><b>Knowledge=People+Information</b></a><br />
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For more science community details see previous posts on the key topics: <a href="http://miningdrugs.blogspot.be/2012/01/top-10-misconceptions-in-science.html">communication</a>, <a href="http://miningdrugs.blogspot.be/2009/12/social-media-needs-to-support-different.html">social media</a>, utilizing <a href="http://miningdrugs.blogspot.be/2009/01/collaboration-bullseye-20-information.html">community knowledge management (collaboration bullseye 2.0)</a>, and <a href="http://miningdrugs.blogspot.be/2009/09/innovation-20-looking-for-strategy-in.html">innovation</a>. <br />
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<h3>
No, "drug space" scientists alone will not be able to handle exponential data growth</h3>
As discussed many times, scientific data growth is literally exploding by any metric (<a href="http://www.ncbi.nlm.nih.gov/genbank/genbankstats.html">GenBank</a>, <a href="http://www.pdb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100">RCSB</a>, <a href="http://blogs.nature.com/news/thegreatbeyond/2009/09/50_million_chemicals_and_accel_1.html">Chemistry</a>, <a href="http://nar.oxfordjournals.org/content/vol38/suppl_1/index.dtl">Bioinf DB</a>, <a href="http://www.nature.com/nature/journal/v440/n7083/full/440413a.html">science in exp. world</a>, <a href="http://www.nature.com/nrm/journal/v10/n11/fig_tab/nrm2787_F1.html">networks</a>, <a href="http://bytesizebio.net/index.php/2010/07/22/protein-function-how-do-we-know-that-we-know-what-we-know/">bio DB</a>). Reading time and processing time of scientists stay typically the same (<i>personal constraint</i>). Since those very same scientists are part of bound organisations (<i>academic or commercial constraint</i>), it becomes even more relevant that we as "drug space" community become smarter and more efficient to exchange information by reducing barriers with more "open" standards, and "open" mindset being supported with proper <a href="http://www.slideshare.net/joergkurtwegner/science-and-compliant-commenting">collaboration management</a> preventing fear and being non-compliant. Finally, and again, "open" must not mean "for free".<br />
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<h3>
Yes, I care about usability of data more than just the amount of it</h3>
As said on the original "<a href="http://blog.computationalcomplexity.org/2011/01/is-cheminformatics-new-bioinformatics.html">Is Cheminformatics the new Bioinformatics?</a>" thread: If I personally would believe the amount of data is more relevant than its relevance for people, and especially patients, out there, we should all start analysing YouTube videos and not drug data from limited patient groups. Again, dear -informatics reader, no technology alone will not cut it, if not connected with more scientists out there. Surely, large-scale mining is important, but we have to deal with complex systems and being able to work with them is not only a matter of scalability, but of true collaboration with much more partners and experts, supported by technology. So, please do not come again with the argument that everyone in the "drug industry" has to learn from the "chip industry". No, it is rather the other way around, people in the chip industry have to understand the <a href="http://miningdrugs.blogspot.be/2007/11/andy-grove-when-silicon-indoctrinates.html">complexity and challenges of living systems</a>.<br />
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<h3>
<b>References</b></h3>
<ul>
<li>Joerg Kurt Wegner, Aaron Sterling, Rajarshi Guha, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel O'Boyle, John Overington, Herman Van Vlijmen, and Egon Willighagen. 2012. Cheminformatics. Commun. ACM 55, 11 (November 2012), 65-75.</li>
<li>via <a href="http://dx.doi.org/10.1145/2366316.2366334">DOI 10.1145/2366316.2366334</a></li>
<li>via <a href="http://www.citeulike.org/user/egonw/article/11546578">CiteULike</a></li>
</ul>
Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-90319757347684638382012-10-07T17:02:00.001+02:002012-10-07T17:09:24.565+02:00Drug resistance (brief clarification)<div style="text-align: justify;">
Some of my science peers contacted me and therefore I would like to add some clarification to the "drug resistance" statement following after 0:44 in the following video.
We need to separate a bit more cause and consequence in the mentioned HIV drug resistance design context:</div>
<blockquote>
It is not the drug that changes, but the virus, bacteria, or host system that changes! Drug resistance is an evolutionary consequence of quickly changing viruses.</blockquote>
As <a href="http://en.wikipedia.org/wiki/Drug_resistance">Wikipedia states</a> correctly<br />
<blockquote>
Drug or toxin or chemical resistance is a <b>consequence of evolution</b> and is a response to pressures imposed on any living organism. Individual organisms vary in their sensitivity to the drug used and some with greater fitness may be capable of surviving drug treatment. <b>Drug-resistant traits are accordingly inherited by subsequent offspring</b> (of a virus, bacteria, or host system), resulting in a population that is more drug-resistant.</blockquote>
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For HIV the design goal is to create a drug that is able to work therefore not against a single virus, but rather a spectrum of virus populations (in a single patient) that might occur in the future as a cause of virus evolution. Besides of improving the activity spectrum of a single drug are HIV patients typically also taking several drugs, often three or four, known as <a href="http://en.wikipedia.org/wiki/Management_of_HIV/AIDS">highly active antiretroviral therapy</a>, or HAART. HAART decreases the amount of HIV and rebuilds the immune system, since it able to suppress various HIV sub-populations much better.
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<iframe allowfullscreen="allowfullscreen" frameborder="0" height="315" src="http://www.youtube.com/embed/1AJKcoVFpeU" width="560"></iframe><br /></div>
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Besides the above clarification might it be interesting for many people to place the research and design process of drugs in the full "from molecule to medicine" process as outlined in the following video. Another important aspect being mentioned there is the <a href="http://en.wikipedia.org/wiki/ADME">ADME</a> profile of drugs and the design process to improve it.</div>
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<iframe allowfullscreen="allowfullscreen" frameborder="0" height="315" src="http://www.youtube.com/embed/ypZO2gEHI2M" width="560"></iframe><br /></div>
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Overall, there are various design stages and multiple departments and rationals involved, and this is therefore a complex, iterative, highly collaborative, and time consuming process as explained in the second video. We are on it ...</div>
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"Our work is only finished when the patient is genuinely cured." [<a href="http://www.linkedin.com/in/joergkurtwegner">Joerg Kurt Wegner</a>]</blockquote>
Please let me know, if you have any additional comments.Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-89039122646207189602012-05-18T18:27:00.000+02:002012-05-18T18:27:09.309+02:00Job offer - Chemogenomics Scientist - Janssen - Spain<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://bks6.books.google.be/books?id=KC5_LjSY_5EC&printsec=frontcover&img=1&zoom=1&edge=curl&imgtk=AFLRE71HDHXswdvZuDYRBA1SE-AFB2hxddldAi1No7jtSPukmA53YfMzHR484-480pNh7B1LGdXLtxWcbKhCY3Iw2wYkyu3W1EytByOkPPLpnVcQFhUOfVrqu3_otStAlCol0lkwg5tA" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A <a href="http://books.google.be/books/about/Chemogenomics_In_Drug_Discovery.html?id=KC5_LjSY_5EC">Chemogenomics book</a> for getting started.</td></tr>
</tbody></table>
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<span id="goog_1601997791"></span><span id="goog_1601997792"></span><a href="http://www.blogger.com/"></a></div>
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Original <a href="https://jnjc.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=61692">Janssen job offer</a> under ID 00000599, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=chemogenomics">Chemogenomics </a>Scientist.<br />
Job offer on <a href="http://www.ccl.net/cca/jobs/joblist/mess0024232.shtml">CCL.net</a>.<br />
<br />
<b>Description</b><br />
<a href="http://en.wikipedia.org/wiki/Janssen_Pharmaceutica">Janssen Pharmaceuticals</a>, Inc., a pharmaceutical company of Johnson & Johnson, provides medicines for an array of health concerns in several therapeutic areas, including: attention deficit hyperactivity disorder (ADHD), cardiovascular disease, general medicine (acid reflux disease, infectious diseases), mental health (bipolar I disorder, schizophrenia), neurologics (Alzheimer's disease, epilepsy, migraine prevention and treatment), pain management, and women's health. Our ultimate goal is to help people live healthy lives. We have produced and marketed many first-in-class prescription medications and are poised to serve the broad needs of the healthcare market - from patients to practitioners, from clinics to hospitals. For more about Janssen Pharmaceuticals, Inc., one of the Pharmaceutical Companies of Johnson & Johnson.<br />
<br />
<b>About the job</b><br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=chemogenomics">Chemogenomics research</a> includes several areas of new science at the interface of chemical compounds and genome-wide sets of (or families of) genes and/or proteins. Instead of the more traditional "single target" - "multiple compounds" computational modeling approaches, chemogenomics looks more broadly at target space, and aims to predict the set of proteins with which compounds interact. This approach has many applications, including phenotypic screen target deconvolution, to polypharmacology, to early prediction of toxicity.
Another area of interest is the more complex experimental data that are generated for chemical compounds, by technologies like microarray or RNAseq gene expression data, high-content imaging readouts, metabolomics, proteomics, etc. Discovering relationships between chemical structures and these complex experimental data requires different approaches than traditional molecular modeling techniques, and may involve network modeling, advanced data mining techniques, pattern recognition approaches, etc. The ultimate goal is to be able to use these complex experimental readouts in the optimization of compounds, and the person in this position will play an important role in developing that expertise.<br />
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<b>Tasks</b><br />
<ul>
<li>Develop new computational approaches and models for the prediction and analysis of interactions between small molecules and sets of genes and/or proteins </li>
<li>Apply computational techniques to the prediction of targets for chemical compounds, for use in the deconvolution of phenotypic compound screens, polypharmacology, early detection of possible toxicity, etc. </li>
<li>Computationally analyze the relationships between chemical structures and various high-dimensional assay readouts such as gene expression, high content imaging, metabolomics, etc. </li>
<li>Compound design based on target- or target-family based predictive computational modeling </li>
</ul>
<b>Qualifications</b><br />
<ul>
<li>PhD in Computational Chemistry or Computational Biology, or related field. Several years (3+) of industrial experience is desirable. </li>
<li>Experience with Chemogenomics research highly desirable, for example in computational deconvolution of phenotypic screen data or analysis of relationships between chemical structure and gene expression. </li>
<li>Knowledge of molecular networks in the cell, and network modeling techniques is desirable.
· Hands-on experience with relevant computational tools and databases. Ability to program and/or write scripts. </li>
<li>Excellent communication, reporting and team working skills </li>
</ul>
<b>Primary Location</b><br />
<a href="http://en.wikipedia.org/wiki/Toledo,_Spain">Europe/Middle East/Africa-Spain-Castille-La Mancha-Toledo</a><br />
<b><br /></b><br />
<b>Organization </b><br />
Janssen-Cilag S.A. (formerly Janssen Sp) (7300)<br />
<b><br /></b><br />
<b>Job Function</b><br />
InformaticsAnonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0Plaza del Ayuntamiento, 1, 45002 Toledo, Spanje39.8567775 -4.024475939.808274 -4.1030969 39.905281 -3.9458548999999996tag:blogger.com,1999:blog-26255983.post-73856193032959981112012-01-02T14:35:00.015+01:002012-02-15T19:54:38.819+01:00Top 10 misconceptions in science communicationI would like to trigger some warnings about typical misconceptions in personal science communication. I have read the blog posts of <a href="https://plus.google.com/109222112653465205941/posts/cb1T8D2K9hN">Tony</a> and <a href="http://www.science3point0.com/mcblawg/2012/01/02/social-networking-tools-for-scientists-or-how-to-brand-yourself-online-as-a-digital-citizen/">Graham</a> about social networking tools for scientists, and got indeed left with the feeling that it is all about tools and the right databases. To be clear, it is not! I have, of course, also read the books about <a href="http://books.google.be/books?id=Bj9lzuJIqbwC">Collaborative Computational Technologies for Biomedical Research</a> and <a href="http://books.google.be/books?id=afqfFW8WV9cC">Reinventing Discovery</a>. One thing is very clear, it is not about information (tools/data) alone, it is not about people alone, but <span style="font-weight:bold;">Knowledge=People+Information</span>:<blockquote>People learn in response to need. When people cannot see the need for what's being taught, they ignore it, reject it, or fail to assimilate it in any meaningful way. [<a href="http://www.joergkurtwegner.eu/?q=node/7">Social media needs to support different scientific personalities</a>]</blockquote>I can understand that many scientists might not have a lot of experience with PIM or KM (Personal Information Management or Knowledge Management), since it sounds unsexy for many researchers and research grants. Still, maybe some science-sustainability thinking would be good, otherwise we are facing more <a href="http://www.ncbi.nlm.nih.gov/pubmed/18819940">data tombs</a>, either in science <a href="http://www.ncbi.nlm.nih.gov/pubmed/18413326">information</a>, science <a href="http://plindenbaum.blogspot.com/2010/05/poor-state-of-java-web-services-for.html">services</a>, or personal expert profiles.<br /><br />Now, here the <span style="font-weight:bold;color:#FF5500;">top 10 of misconceptions in science communication</span>:<br /><br /><span style="font-weight:bold;color:#FF5500;">1. People know how to find me.</span><br />Then you must have a very unique name and are assuming that all others are already knowledge ninjas. In reality have most other people troubles finding, re-finding <a href="http://kftf.ischool.washington.edu/index.htm">information (credits:KFTF)</a> or <a href="http://www.slideshare.net/CameronNeylon/oh-youre-that-cameron-neylon">people (credits:Cameron Neylon)</a>.<br /><br /><span style="font-weight:bold;color:#FF5500;">2. People make extra efforts in finding me or my research results.</span><br />Forget it! Most of us are drowing in information and workplace/private distractions. Most of us are <a href="http://books.google.be/books?id=QgzBqhbdlvUC">already exhausted</a>. So, if you want that others read more information about yourself or your research results, make it easy for them getting, finding, and re-finding it. Yes, this might require some learning from you on how to make it easier for others. For making the cognitive surplus possible everyone needs to understand the limitations of human potential and how to change behavior and current practice. I fully agree with <a href="http://www.goodreads.com/book/show/7614793-cognitive-surplus">Shirky's vision</a> on this.<br /><br /><span style="font-weight:bold;color:#FF5500;">3. My university profile page is persistent and a good expert profile maintenance scenario.</span><br />Then why are asking publishers for your email and institute and not for your profile page? There is a reason the science community is interested in ORCID (Open Researcher and Contribution ID)! Please check some of <a href="http://www.slideshare.net/mfenner">Martin Fenner</a>'s slides to learn more.<blockquote>ORCID aims to solve the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. [<a href="http://orcid.org/">ORCID.org</a>]</blockquote>Besides, how stable is a university group profile when changing groups? Yes, there are more persistent expert profile and expert activity solutions out there, use them.<br /><br /><span style="font-weight:bold;color:#FF5500;">4. I am a scientist and journal publications are sufficiently granular as communication form.</span><br />Oh really? We know that people <a href="http://www.slideshare.net/joergkurtwegner/science-communication-university-of-antwerp/12">loose interest in scientific publications</a> rather quickly. Why should your publications be the exception? Get over it and be realistic, it is not about you, it is about the crowd, so go where the crowd is, and <a href="http://www.ncbi.nlm.nih.gov/pubmed/21672971">question/answer systems</a> are clearly one possibility for sharing your expert knowledge in more incremental ways. There is no 'one size fits all', if I have a simple question, do I really need to read all your publications? Think about it...<br /><br /><span style="font-weight:bold;color:#FF5500;">5. Social media technology will fix all your problems.</span><br />Nope, at the end of the day it is about people collaborating with another. Technology just serves as amplifier.<blockquote>If you do not enter the groundswell with a clear goal you will fail. [<a href="http://www.goodreads.com/book/show/2896061-groundswell">Groundswell</a>]</blockquote> So, what is your goal?<br /><br /><span style="font-weight:bold;color:#FF5500;">6. Sharing information is good enough.</span><br />People want knowledge, but for getting it they have to make sense of information and learn. So, just sharing information requires to spend time for making sense out of it and taking it in. There is a reason for caring about <a href="http://ewh.ieee.org/soc/pcs/index.php?q=node/111">effective presentations (MP3, credit: Jean-Luc Doumont)</a>. Yes, the web is one way to present things to others. Please <a href="http://www.principiae.be/">make an effort structuring your thoughts</a> and I can also recommend the following book offering some help: <a href="http://www.treesmapsandtheorems.com/">Trees, maps, and theorems - Effective communication for rational minds</a>.<br /><br /><span style="font-weight:bold;color:#FF5500;">7. Sharing raw data is good enough.</span><br />If information sharing (point 6.) requires efforts from others to take it in, do you then really think sharing raw data will require less efforts? In the contrary, it takes even more efforts, and please be aware that <a href="http://www.keepingfoundthingsfound.com/">people are different, so are their information management behaviours</a>. Right, it is not about you, alone, it is about them!<br /><br /><span style="font-weight:bold;color:#FF5500;">8. If I become or make 'Open XYZ' everybody will come to me.</span><br />Simply, no! I clearly agree that open research, <a href="http://rcsproject.wordpress.com/reports/">communication</a>, <a href="http://www.opensourcejahrbuch.de/setLang?lang=en">source</a>, and data helps in extending collaboration networks, but just making things 'open' is not a sufficient strategy.<br /><br /><span style="font-weight:bold;color:#FF5500;">9. Hope (for altruism) is a strategy.</span><br />No, and especially in science the crowds are becoming more specialized and smaller. Do you remember that we had such discussions before?<blockquote><a href="http://friendfeed.com/the-life-scientists/e5445f3b/i-will-start-my-own-attempt-for-crowdsourcing">What are the measures that can make community genome annotation a success?</a></blockquote> Without <a href="http://www.joergkurtwegner.eu/?q=altruisticscience">measuring and caring for contributions of others and their peers</a>, you will fail. You have your own site and data, fine, and can others integrate it into their networks? Think about their metrics, yours is secondary!<br /><br /><span style="font-weight:bold;color:#FF5500;">10. There is a free lunch, and everything I do is already supporting others in their needs.</span><br />Then you are clearly able to handle that people have more and more choice and run with what <a href="http://en.wikipedia.org/wiki/Long_Tail">is best for them</a>, congratulations! You know that free means <a href="http://www.goodreads.com/book/show/6150530-free">that free</a>!<br /><br /><b>More reading</b><br />Much more insights can be found in various related books, check my <a href="http://www.goodreads.com/review/list/2075610">reading list</a>. As a shortcut, I am always happy to talk, present, or collaborate with you.Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com1tag:blogger.com,1999:blog-26255983.post-69412511362261533622011-03-06T19:08:00.014+01:002011-03-06T20:39:40.620+01:00Should scientists care about a Wiki for Knowledge Management?I would like to encourage scientists to contribute to the <a href="http://survey.nitens.org/?sid=21693">ongoing survey</a> of the Research Committee of the Wikimedia Foundation. The title of the survey is "Expert barriers to Wikipedia?" and you as scientists, experts, would greatly help in understanding what drives people to contribute, collaborate, and communicate with each other. The focus of their survey is on Wikipedia as Knowledge Management (KM) platform.<br /><a href="http://survey.nitens.org/?sid=21693"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 125px; height: 125px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj33oMKW6DrUB_24lKP3dS1zSuY8O57EHaFqKOZFJMUPtc0L0jYolCOiw91B1mYWfcxpQvxLtf_p1TqW05tqKMXyzX8XHJ1vDXXcQaTNPQmT2-VphWMsFCrYgthsawbYnnAf5ij/s320/acawp.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5581051827744969330" /></a><br />I took the survey and add here additional remarks to some science specific issues:<br /><ul><li>We have featured articles on Wikipedia. Do we also have "expert approved" articles? If not, could the <a href="http://meta.wikimedia.org/wiki/Research_Committee">WM:ResearchCommittee</a> create some guidelines, and expert networks in taking this post-review on? This would help having a better argument against those typical "Is WP a reliable source?" discussions, especially if it comes to "expert topics", e.g. medical or scientific topics.</li><li>Journal articles and conference articles can be cited and have unique <a href="http://en.wikipedia.org/wiki/Digital_object_identifier">Digital Object Identifiers</a>. Can each WP article ensure getting a proper citable DOI?</li><li>What is the <a href="http://en.wikipedia.org/wiki/Impact_factor">impact factor</a> for WP? If it only applies to journals, then what would be required for enabling a WP:Journal? Besides, if there is no number, there is no incentive! Many people typically say this pointing to abusing free-riders and <a href="http://www.joergkurtwegner.eu/?q=altruisticscience">Altruism should not be overrated</a>, since conditional collaborators (the largest crowd) will only contribute when they do not feel abused by free-riders. Besides, expert recognition from other experts is critical, too.</li><li>Edit counts on WP are easy to calculate, but how do we compare expert contributions from correcting spelling errors? Do not get me wrong, every contribution counts, I agree with Shirky that " the smallest creative act, is still a creative act". Anyway, some experts care a lot for being recognized as an expert contributor, if this is not the case, they might turn from being <a href="http://www.joergkurtwegner.eu/?q=altruisticscience">"conditional collaborators" to "non-collaborative"</a> WP users.</li></ul>Finally, Let us never forget that <a href="http://www.joergkurtwegner.eu/?q=node/7">Knowledge=People+Information</a>, so WP:Wiki technology alone will not move anywhere, if people cannot see the need for it, or do not get the kudos they deserve in a proper peer-recognition manner. If people get the feeling that there is no audience or not the right audience caring for contributions, people simply stop contributing.<div><br /><div>The following two slide decks fit into this discussion of a "Wikipedia-Myth", and some might prefer looking at them for stimulating thoughts about Wikipedia as KM platform.</div><div><b>Let us know what you think by contributing to the <a href="http://survey.nitens.org/?sid=21693">WM:Survey</a> or comment below</b> and we will forward your thoughts to the WM:ResearchCommittee.</div></div>Thank you!<div style="width:425px" id="__ss_1135966"> <strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/TSystemsMMS/enterprise-20-knowledge-management-the-wikipedia-myth-1135966" title="The Wikipedia Myth - Enterprise 2.0 Knowledge Management">The Wikipedia Myth - Enterprise 2.0 Knowledge Management</a></strong> <object id="__sse1135966" width="425" height="355"> <param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=wissensmanagement1englischneu-090312064725-phpapp01&stripped_title=enterprise-20-knowledge-management-the-wikipedia-myth-1135966&userName=TSystemsMMS"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <embed name="__sse1135966" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=wissensmanagement1englischneu-090312064725-phpapp01&stripped_title=enterprise-20-knowledge-management-the-wikipedia-myth-1135966&userName=TSystemsMMS" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed> </object> <div style="padding:5px 0 12px"><strong style="display: inline !important; margin-top: 12px; margin-right: 0px; margin-bottom: 4px; margin-left: 0px; "><a href="http://www.slideshare.net/TSystemsMMS/enterprise-20-knowledge-management-people-at-the-center" title="Enterprise 2.0 Knowledge Management - People at the Center">Enterprise 2.0 Knowledge Management - People at the Center</a></strong></div></div><div style="width:425px" id="__ss_1136056"> <object id="__sse1136056" width="425" height="355"> <param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=wissensmanagement2englischneu-090312070622-phpapp01&stripped_title=enterprise-20-knowledge-management-people-at-the-center&userName=TSystemsMMS"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <embed name="__sse1136056" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=wissensmanagement2englischneu-090312070622-phpapp01&stripped_title=enterprise-20-knowledge-management-people-at-the-center&userName=TSystemsMMS" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed> </object></div>Did you already take the survey? Just checking ... ;-)<a href="http://survey.nitens.org/?sid=21693"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 125px; height: 125px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj33oMKW6DrUB_24lKP3dS1zSuY8O57EHaFqKOZFJMUPtc0L0jYolCOiw91B1mYWfcxpQvxLtf_p1TqW05tqKMXyzX8XHJ1vDXXcQaTNPQmT2-VphWMsFCrYgthsawbYnnAf5ij/s320/acawp.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5581051827744969330" /></a>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-67226754752368228102011-01-09T17:28:00.007+01:002011-01-09T17:48:05.679+01:00Life Science in 2020 - Vision of students joining ESOF 2010Here <a href="http://www.sciencebus.se/">more information</a> about the Janssen ScienceBus 2010 to the ESOF conference (<a href="http://www.esof2010.org">EuroScience Open Forum</a>).<div><ul><li><a href="http://www.sciencebus.se/Sciencebus/ESOF2010_files/ScienceBus.Booklet.pdf">Life Science in 2020</a> - Vision of the students</li><li><a href="http://www.sciencebus.se/Sciencebus/Startsida_files/Alfons_Boesmans_Booklet.pdf">Booklet</a> from Alfons Boesmans</li></ul><div style="text-align: center;"><object width="425" height="257"><embed src="http://www.youtube.com/v/0931jCHMP00?fs=1&hl=nl_NL" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="257"></embed></object></div><b>See also</b><br /><div><ul><li><a href="http://www.joergkurtwegner.eu/?q=node/12">Answers to discussions with students and photos</a></li><li><a href="http://www.joergkurtwegner.eu/?q=node/11">Remarkable sentences</a></li><li><a href="http://www.joergkurtwegner.eu/?q=scientific_web_presence">Scientific presence (web)</a></li></ul></div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-15886684764250307142010-11-11T12:01:00.004+01:002010-11-11T12:23:48.536+01:00It's not filter failure. It's a discovery deficit.Great <a href="http://en.wikipedia.org/wiki/Lawrence_Lessig">Lessig</a> styl'ish presentation <a href="http://friendfeed.com/cameronneylon">@Cameron</a>.<br /><blockquote>"<i>Don’t think about filtering.<br />Don’t think about control.<br />Enable discovery.</i>"</blockquote>I simply agree, and we need more "<a href="http://miningdrugs.blogspot.com/2009/12/social-media-needs-to-support-different.html">need alignment</a>" discussions and sufficient resources for making this possible! Aka, I consider a discovery deficit as a lack of enabling true network building and network maintenance scenarios.<br /><div style="width:425px" id="__ss_5731939"><strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/CameronNeylon/its-not-filter-failure-its-a-discovery-deficit" title="It's not filter failure. It's a discovery deficit.">It's not filter failure. It's a discovery deficit.</a></strong><object id="__sse5731939" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=rluk-nov-10-slideshare-101110170845-phpapp02&stripped_title=its-not-filter-failure-its-a-discovery-deficit&userName=CameronNeylon"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed name="__sse5731939" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=rluk-nov-10-slideshare-101110170845-phpapp02&stripped_title=its-not-filter-failure-its-a-discovery-deficit&userName=CameronNeylon" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px">View more <a href="http://www.slideshare.net/">presentations</a> from <a href="http://www.slideshare.net/CameronNeylon">Cameron Neylon</a>.</div></div><script src="http://b.scorecardresearch.com/beacon.js?c1=7&c2=7400849&c3=1&c4=&c5=&c6="></script><br /><b>For related posts see also</b><br /><script src="http://b.scorecardresearch.com/beacon.js?c1=7&c2=7400849&c3=1&c4=&c5=&c6="></script><div><ul><li><a href="http://miningdrugs.blogspot.com/2010/02/friend-of-friend-how-to-create-foaf.html">FOAF</a> - a decentralized solution for knowledge=people+information</li><li>Social media and science personalities, let us align <a href="http://miningdrugs.blogspot.com/2009/12/social-media-needs-to-support-different.html">our needs</a> and ensure <a href="http://miningdrugs.blogspot.com/2009/05/peer-recognition-and-building.html">building relationships</a></li><li><a href="http://miningdrugs.blogspot.com/2009/09/innovation-20-looking-for-strategy-in.html">Innovation 2.0</a>, especially in drug design</li><li>Information overload is a challenge we have to work on in science, e.g. via <a href="http://miningdrugs.blogspot.com/2009/01/collaboration-bullseye-20-information.html">Enterprise 2.0 strategies</a></li><li>Only, if we work on all of those things we can enable <a href="http://miningdrugs.blogspot.com/2007/11/six-rules-for-creating-data-driven-drug.html">data-driven</a> and <a href="http://miningdrugs.blogspot.com/2007/09/six-sigma-in-drug-design-old-hands-or.html">six-sigma-driven</a> drug design</li></ul></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-16015816356326096962010-09-01T20:13:00.009+02:002010-09-01T20:49:59.713+02:00Science plog'ing, S3'ing, and other trendsAfter the <a href="http://scienceblogs.com/clock/2010/07/scienceblogs_and_me_and_the_ch.php">Pepsi scandal</a> in the scientific community it is nice to see that the scientific bloggers are moving on and yes<br /><blockquote>"If science bloggers (and blogging networks) work together, we can reach for the stars" [<a href="http://twitter.com/mfenner/status/22728198402">@mfenner</a>]</blockquote>Two recently launched blogging networks are<br /><br /><a href="http://www.science3point0.com/">Science 3.0<img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 107px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4ImmdOQHjS3QCwTVz6pablCrz6xieoc0DBzQoN5CvImTXsUnQ8iU2HKoDvPVnMDZllAtzicfzhNwQZSWyV35i3Wqt2Iw-eAquZciTe2n7frxmneujJToeSMofqhTtyXW4iQ2J/s320/1280388949-science3point0logo.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5512014250968480370" /></a><br /><a href="http://blogs.plos.org/">PLoS blogs<img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 64px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEftVZtT_5quyrc4c5tF1qOsEq1DbcQqe26IgC2JcpRIPZW565Wp13GEmZ3suR46xCrAIcm67m621LVHJz5OMuHBYw-kvP8KvX9Y7GCQXrq17pmz61q70hX8VXEBiSqoATisLV/s320/plos_logo.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5512014421639856178" /></a>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-51432063583865166702010-05-08T21:21:00.006+02:002010-05-08T23:35:11.872+02:00Molecular design and molecular modeling basicsAfter a recent question on <a href="http://blueobelisk.shapado.com/">Blue Obelisk Exchange</a> and <a href="http://lab.chempedia.com/">ChemPedia Lab</a> about <a href="http://blueobelisk.shapado.com/questions/molecule-modifications-in-drug-design-why">molecular drug design</a> (see also <a href="http://lab.chempedia.com/questions/189/molecule-modifications-in-drug-design-why">cross-post</a>) and a recent book about <a href="http://molecularmodelingbasics.blogspot.com/2010/04/book-is-out.html">molecular modeling basics</a> I thought it is time highlighting more information on that topic.<div><br /></div><div><span class="Apple-style-span" style="font-size:large;">Drug design principles, molecular modeling, and use in medicinal chemistry:</span></div><div><ul><li>C. Bissantz, B. Kuhn, and M. Stahl, A Medicinal Chemist’s Guide to Molecular Interactions, <i>J. Med. Chem.</i>, <b>2010</b>, Article ASAP. DOI <a href="http://dx.doi.org/10.1021/jm100112j">10.1021/jm100112j</a><br /></li><li><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=bioisosterism%5BAll%20Fields%5D&cmd=DetailsSearch">Bioisosterism</a> and bioisosteric design principle articles.</li><li>J. H. Jensen, <a href="http://molecularmodelingbasics.blogspot.com/2010/04/book-is-out.html">Molecular modeling basics</a>, <b>2010</b>.</li></ul><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://farm5.static.flickr.com/4002/4428987368_ba5de9d23a_m_d.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 159px; height: 240px;" src="http://farm5.static.flickr.com/4002/4428987368_ba5de9d23a_m_d.jpg" border="0" alt="" /></a><br /><div><span class="Apple-style-span" style="font-size:large;">Summary slides about molecular modeling (quantum chemistry) of <a href="http://baoilleach.blogspot.com/">Noel O'Boyle</a>:</span></div><div style="width:425px" id="__ss_3902470"><object id="__sse3902470" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-100429094349-phpapp01&stripped_title=quantum-chemistry"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed name="__sse3902470" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-100429094349-phpapp01&stripped_title=quantum-chemistry" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px"><br /></div></div><div style="width:425px" id="__ss_3902503"><object id="__sse3902503" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-ii-100429094643-phpapp01&stripped_title=quantum-chemistry-ii"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed name="__sse3902503" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-ii-100429094643-phpapp01&stripped_title=quantum-chemistry-ii" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px"><br /></div></div><div style="width:425px" id="__ss_3902538"><object id="__sse3902538" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-iii-100429095047-phpapp01&stripped_title=quantum-chemistry-iii"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed name="__sse3902538" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=quantumchem-iii-100429095047-phpapp01&stripped_title=quantum-chemistry-iii" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px"><br /></div></div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com3tag:blogger.com,1999:blog-26255983.post-46084274896989477922010-02-08T12:20:00.015+01:002012-02-09T21:41:17.865+01:00Friend of a friend - How to create a FOAF science network?<div>I strongly believe in <blockquote><a href="http://miningdrugs.blogspot.com/2009/09/innovation-20-looking-for-strategy-in.html"><b><span class="Apple-style-span" style="font-size:large;">Knowledge = People + Information</span></b></a></blockquote></div><div>Thus one critical key aspect is allowing me and my friends (people) finding each other and browsing the information from each other easily. One of the most person-centric ways of defining people-networks are <a href="http://en.wikipedia.org/wiki/FOAF_(software)">friend-of-a-friend (FOAF)</a> networks. Here is why:</div><div><ul><li>First, this is independent of any social networking provider, which might not allow you tracking and entering all the information you need into their system. </li><li>Second, there are multiple ways how you can create FOAF ontologies, e.g. <a href="http://identi.ca/">identi.ca</a>, <a href="http://www.quatuo.com/">Quatuoa</a>, and Pierre's XSL transformation from a <a href="http://plindenbaum.blogspot.com/2010/02/linkedinxslt-foaf-people-from.html">LinkedIn profile</a>. I used the following starting points<br /><ul><li><a href="http://en.wikipedia.org/wiki/FOAF_(software)">FOAF</a></li><li>Description Of A Career (<a href="http://en.wikipedia.org/wiki/Description_of_a_Career">DOAC</a>) entries from my LinkedIn profile using <a href="http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/linkedin2foaf.xsl">Pierre's XSL</a></li><li>Finally, I placed <a href="http://github.com/joergkurtwegner/snippets/blob/master/xml/foaf.xml">my FOAF profile on GIT</a>, please feel free using this as starting point for your FOAF profile.</li></ul></li><li>Third, put your FOAF profile on any web-server and <a href="http://wiki.foaf-project.org/w/Autodiscovery">enable autodetection</a> from your sites, and your semantic people network is ready! Note that Google is allowing you to import FOAF ontologies into Google profiles. Since this information can be used for searching within your <a href="http://ff.im/f7zfE">social circle</a>, this clearly facilitates finding each other and finding information within social networks.</li><li>Fourth, there are multiple visualization and browsing options for FOAF networks, e.g. <a href="http://xml.mfd-consult.dk/foaf/explorer/?foaf=http://www.joergkurtwegner.de/">FOAF browser</a>.</li></ul></div><div>I enabled those visualizations on my blog and homepage using the logos below, please feel free to check the output when clicking on them: </div><div><br /></div><div><div style="text-align: right;"></div><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://xml.mfd-consult.dk/foaf/explorer/?foaf=http://www.joergkurtwegner.eu"></a><a href="http://xml.mfd-consult.dk/foaf/explorer/?foaf=http://www.joergkurtwegner.eu"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 240px; height: 240px;" src="http://www.joergkurtwegner.de/images/foaf-explorer.png" border="0" alt="" /></a><div style="text-align: right;"><a href="http://xml.mfd-consult.dk/foaf/explorer/?foaf=http://www.joergkurtwegner.eu">FOAF explorer</a></div></div><br /><br /><b><span class="Apple-style-span" style="color:#990000;">Update </span></b>after a discussion with <a href="http://twitter.com/melvincarvalho">@melvincarvalho</a> and <a href="http://twitter.com/yokofakun">@yokofakun</a>:<br /><ul><li>Make sure adding a <a href="http://xmlns.com/foaf/spec/#term_PersonalProfileDocument">foaf:PersonalProfileDocument</a> to your profile. Again, see <a href="http://github.com/joergkurtwegner/snippets/blob/master/xml/foaf.xml">my example</a>.</li><li>Please make sure <a href="http://www.w3.org/RDF/Validator/ARPServlet?URI=http://www.joergkurtwegner.de/foaf.xml&PARSE=Parse+URI:+&TRIPLES_AND_GRAPH=PRINT_TRIPLES&FORMAT=PNG_EMBED">validating your FOAF profile</a> with the W3C RDF validation service.</li><li>There is an option adding <a href="http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/pubmed2rdf.xsl">research papers</a> using the XSL of <a href="http://twitter.com/yokofakun">@yokofakun</a> (I have still not done, yet)</li><li>Finally, here are a few more visualization options:</li><ul><li><a href="http://foaf.me/?webid=http://github.com/joergkurtwegner/snippets/raw/master/xml/foaf.xml">FOAF.me</a> created by <a href="http://twitter.com/melvincarvalho">@melvincarvalho</a></li><li><a href="http://www.foafer.org/?file=http://www.joergkurtwegner.eu/foaf.xml#me">Foafer</a></li><li><a href="http://sig.ma/search?q=http%3A%2F%2Fwww.joergkurtwegner.eu%2Ffoaf.xml%23me">Sig.ma</a></li><li><a href="http://xml.mfd-consult.dk/foaf/explorer/?foaf=http://www.joergkurtwegner.eu">FOAF explorer</a></li></ul></ul>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-3615021624416686772009-12-20T13:21:00.007+01:002009-12-20T13:40:28.556+01:00Social media needs to support different scientific personalities<a href="http://pipeline.corante.com/archives/2009/12/17/why_dont_chemists_communicate_or_do_we.php">Derek</a> started an interesting discussion about social media in chemistry based on a <a href="http://dx.doi.org/10.1038/nchem.448">nature commentary</a>.<br /><br /><span style="font-weight: bold;">Here my comment</span><br />Please let us not forget that there are different 'scientific personalities' [<a href="http://bit.ly/5teuwO">1</a>] as there exist different 'information management personalities' [<a href="http://bit.ly/87qcST">2</a>]. I think we should appreciate the diversity and never even try to force all scientists behaving the same. Nonetheless, would I like to see more scientists contributing to social media. Especially supporting various personalities for various reasons in multiple ways !<br /><br />Now, if scientists do not contribute to social media then for me the question is rather what are we doing wrong in supporting their needs for learning/contributing [<a href="http://bit.ly/XAvjK">3</a>]? Chemistry always was and still is a very (article) reading intense area and I am still wondering if 'information overload' of yet-another-information-channel might be one cause of social media inactivity for the 'older scientist generation'. The youngsters (generation X and Y) are clearly using social media, but might not have the highest scientific profiles, yet, but some of them will have it soon!<br /><br />I think the following quote is very true, what do you think?<br /><blockquote>"People learn in <span style="font-weight: bold;">response to need</span>. When people cannot see the need for what's being taught, they ignore it, reject it, or fail to assimilate it in any meaningful way." [<a href="http://bit.ly/51I8k1">4</a>]</blockquote><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://bit.ly/XAvjK"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 230px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5uxeQmKf2c4YckOlZXrXw9Dge8N4ecOgYJg_HXYAtWSD67facNp7kQ8QdX0VmSCthA9k3A7_Wtd7xjZ_ZukTvz71VniC72Jg7ADcSJEySPRd3S4oAG1qwv9aqWrJtgKmBK1u-/s320/knowledge_creation_based_on_need.gif" alt="" id="BLOGGER_PHOTO_ID_5417296881326079922" border="0" /></a><br /><span style="font-weight: bold;">References</span><br />[1] <a href="http://bit.ly/5teuwO">http://bit.ly/5teuwO</a><br />[2] <a href="http://bit.ly/87qcST">http://bit.ly/87qcST</a><br />[3] <a href="http://bit.ly/XAvjK">http://bit.ly/XAvjK</a><br />[4] <a href="http://bit.ly/51I8k1">http://bit.ly/51I8k1</a>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com7tag:blogger.com,1999:blog-26255983.post-73340602684168993052009-12-13T14:57:00.008+01:002009-12-13T15:21:45.761+01:00Sky-rocking graphics in new MOE releaseHave you seen the new graphics functionality in the new MOE (Molecular Operating Environment) of the <a href="http://www.chemcomp.com/">Chemical Computing Group</a> (CCG)? No? You need to look at some examples in their <a href="http://www.chemcomp.com/software-moegallery.htm">image gallery</a>! The graphics engine is by-far the best I have seen since a long time, even without using 3D shutter glasses.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.chemcomp.com/software-moegallery.htm"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 370px; height: 295px;" src="http://www.chemcomp.com/img/moegallery/hin1_4_fb07_rib_cpk_blue.jpg" alt="" border="0" /></a>Besides, the release has not only an improved look-and-feel, but also (as usual) a lot of high-level algorithm improvements. Here an overview about the new features of the <a href="http://www.chemcomp.com/software-moe2009.htm">2009.10 release</a>:<br /><ul><li>Real Time Ray-traced Graphics</li><li>Protein/Antibody Modeling</li><li>LowModeMD Conformational Search</li><li>Synthetic Score Descriptor</li><li>Scaffold Replacement/Fragment Linking </li><li>MOE/web SOAP Server</li></ul>Finally, for those being interested in using <a href="http://www.schrodinger.com/ProductDescription.php?mID=6&sID=33">Schrodinger</a>'s or <a href="http://www.chemcomp.com/">CCG</a>'s tools in combination with <a href="http://www.knime.org/">KNIME</a>, there is good news. After a long period of pushing, the KNIME crew released a <a href="http://www.knime.org/blog/knime-report-designer-released">reporting collection</a> and <a href="http://www.knime.com/blog/knime-enterprise-products">enterprise products</a>, e.g. server and cluster executions. This is definitely a step towards business intelligence and certainly an important achievement of the development and strategic planning team.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.knime.org/"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 377px; height: 150px;" src="http://www.knime.org/files/framework_logo_150.jpg" alt="" border="0" /></a>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-30732627778409437192009-11-07T13:34:00.007+01:002009-11-07T14:20:10.098+01:00Warren DeLano - In MemoriamThe family of Warren Lyford DeLano has created a "<a href="http://web.me.com/brendandelano/Warren_Lyford_DeLano/In_Memorium.html">In Memorium</a>" page and <a href="http://warrendelano.blogspot.com/2009/11/my-brother-warren.html">blog</a>. Please share your memories there !<div><br /></div><div>As many others, I am shocked, sad, and are left with the impression having lost something important. We never met in real-life, but exchanged thoughts in several forums, eMails, and other new generation media. He was a natural leader in the life science informatics community (<a href="http://pymol.sourceforge.net/">PyMol</a>, <a href="http://dx.doi.org/10.1016/S1359-6446(04)03363-X">open source</a>) and paved a way for many of us. He will never be forgotten !<br /><br /><b>Twitter </b><a href="http://twitter.com/#search?q=warren%20delano"><b>reactions</b></a><br /><div style="text-align: center;"><a href="http://www.wordle.net/show/wrdl/1309284/Warren_DeLano_Died_-_Twitter_reactions" title="Wordle: Warren DeLano Died - Twitter reactions"><img src="http://www.wordle.net/thumb/wrdl/1309284/Warren_DeLano_Died_-_Twitter_reactions" alt="Wordle: Warren DeLano Died - Twitter reactions" style="padding:4px;border:1px solid #ddd" /></a></div><br /><b>Blog reactions</b><br /><div style="text-align: center;"><a href="http://www.wordle.net/show/wrdl/1309280/Warren_DeLano_Died_-_Blog_reactions" title="Wordle: Warren DeLano Died - Blog reactions"><img src="http://www.wordle.net/thumb/wrdl/1309280/Warren_DeLano_Died_-_Blog_reactions" alt="Wordle: Warren DeLano Died - Blog reactions" style="padding:4px;border:1px solid #ddd" /></a></div><div style="text-align: left;"><ul><li><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=CCP4BB&T=0&F=&S=&P=36074">CCP4BB Archive</a> </li><li><a href="http://depth-first.com/articles/2009/11/06/warren-delano">Depth-First</a></li><li><a href="http://practicalfragments.blogspot.com/2009/11/remembering-warren-delano.html">Practical fragments</a></li><li><a href="http://shirleywho.wordpress.com/2009/11/07/in-memoriam-warren-delano/">I was lost but now I live here</a> </li><li><a href="http://www.macresearch.org/memoriam-warren-l-delano">MacResearch</a></li><li><a href="http://mndoci.com/2009/11/05/warren-delano-passes-away/">b|b|g|m</a></li><li><a href="http://www.p212121.com/2009/11/05/passing-of-warren-delano/">P212121</a></li><li><a href="http://www.chemspider.com/blog/in-memoriam-warren-delano.html">ChemSpider</a></li><li><a href="http://bytesizebio.net/index.php/2009/11/05/warren-delano/">ByteSizeBio</a></li></ul></div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-81767174626124988772009-09-14T20:21:00.006+02:002009-09-14T21:37:26.029+02:00Innovation 2.0 - Looking for a strategy in drug design and health care?<div><blockquote style="text-align: center;">"<i>You can’t control what you can't measure.</i>" [<a href="http://en.wikipedia.org/wiki/Tom_DeMarco">Tom DeMarco</a>]</blockquote></div>I am strongly believing in people-centric innovation for <a href="http://miningdrugs.blogspot.com/2007/08/six-degrees-of-drug-design-social.html">drug design</a> and health care. Still, we have serious challenges to solve before this can happen, and a lot of them are <a href="http://miningdrugs.blogspot.com/2007/11/andy-grove-when-silicon-indoctrinates.html">in-vivo, not in-silico</a>:<br /><ol><li>Get rid of the <a href="http://miningdrugs.blogspot.com/2009/05/we-know-that-scientific-collaboration.html">negative group dynamics</a>.</li><li>Accept <a href="http://miningdrugs.blogspot.com/2009/01/collaboration-bullseye-20-information.html">information overload</a> and embrace collaboration.</li><li><a href="http://miningdrugs.blogspot.com/2009/05/drug-design-and-thinking-unthinkable.html">Bridge silos</a>, e.g. <a href="http://miningdrugs.blogspot.com/2009/03/bridging-chemistry-islands-to-web-data.html">chemical</a> data silos, but also break-down legal or license hurdles, e.g. by using <a href="http://www.businessinsider.com/henry-blodget-google-launching-micropayments-and-subscription-system-to-save-newspapers-2009-9">micropayments</a>.</li></ol><div>Please find below the slides and handout for my talk in October on the <a href="http://www.bio-itworldexpoeurope.com/">BioIT World conference</a>. The conference will cover a large range of life science topics, e.g. -omics, semantics, technology, bioinformatics, life science software, collaboration platform, etc. This is all very exciting and I am looking forward to those talks and meeting people in real life. </div><div><br /></div><div>Please let me know, if you agree with the challenges, and what you have experienced for using collaboration solutions in a commercial setting. I am a technological geek (tekki), and here I am especially <b>interested in the opinions of the non-tekkis</b> !</div><div><br /></div><div>Talk to you soon ...</div><div><br /></div><div><a href="http://www.slideshare.net/joergkurtwegner/drug-innovation-20-slides" title="Drug Innovation 2.0 (Slides)" style="font: normal normal normal 14px/normal Helvetica, Arial, sans-serif; display: inline !important; margin-top: 12px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; text-decoration: underline; ">Drug Innovation 2.0 (Slides)</a></div><div style="width:425px;text-align:left" id="__ss_1995273"><object style="margin:0px" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=druginnovation2-0-short-090914094243-phpapp02&stripped_title=drug-innovation-20-slides"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=druginnovation2-0-short-090914094243-phpapp02&stripped_title=drug-innovation-20-slides" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="font-size:11px;font-family:tahoma,arial;height:26px;padding-top:2px;">View more <a style="text-decoration:underline;" href="http://www.slideshare.net/">presentations</a> from <a style="text-decoration:underline;" href="http://www.slideshare.net/joergkurtwegner">Joerg Kurt Wegner</a>.</div></div><div style="width:477px;text-align:left" id="__ss_1995272"><a style="font:14px Helvetica,Arial,Sans-serif;display:block;margin:12px 0 3px 0;text-decoration:underline;" href="http://www.slideshare.net/joergkurtwegner/drug-innovation-2-handout" title="Drug Innovation 2 (Handout)">Drug Innovation 2 (Handout)</a><object style="margin:0px" width="425" height="580"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayerd.swf?doc=druginnovation2-handout-090914094249-phpapp01&stripped_title=drug-innovation-2-handout"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayerd.swf?doc=druginnovation2-handout-090914094249-phpapp01&stripped_title=drug-innovation-2-handout" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="580"></embed></object><div style="font-size:11px;font-family:tahoma,arial;height:26px;padding-top:2px;">View more <a style="text-decoration:underline;" href="http://www.slideshare.net/">documents</a> from <a style="text-decoration:underline;" href="http://www.slideshare.net/joergkurtwegner">Joerg Kurt Wegner</a>.</div></div><b>See also</b><div><ul><li>What is an <a href="http://miningdrugs.blogspot.com/2007/05/there-are-too-many-silos-and-often.html">innovation funnel</a> ?</li><li>Is drug design <a href="http://miningdrugs.blogspot.com/2006/10/bounded-rational-drug-design.html">really rational</a> ?</li></ul><br /></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com2tag:blogger.com,1999:blog-26255983.post-89417913063200677132009-09-10T21:07:00.006+02:002009-09-10T22:29:21.082+02:0050 million chemicals, and accelerating - chemical patent overload?(via <a href="http://twitter.com/joergkurtwegner/status/3893561320">NatureNews</a>) As <a href="http://www.cas.org/newsevents/releases/50millionth090809.html">reported</a> by the Chemical Abstract Service (CAS) have they reached 50 million registered chemical entities.<div>Here some numbers to think about</div><div><ul><li>CAS needed 33 years for registering the first 10 million compounds, that is one new compound every 101.5 seconds.</li><li>the last 9 months CAS registered 10 million compounds, in other words, every 2.3 seconds a new compound was created !</li><li>So, chemistry has improved its efficiency 44 times !</li></ul><div><div>This resulted in a drastically increasing patenting rate as mentioned by <a href="http://www.sciencebase.com/science-blog/50-million-chemicals.html">David Bradley</a>. </div><div><br /></div><div>O.k. what happens now to your actual <a href="http://en.wikipedia.org/wiki/Drug_design">lead structure</a> series? </div><div><ol><li>Don't panic! Just get enough money for mining CAS directly ... mmmh ... just kidding.</li><li>Second choice? Extract all 50 million structures from PDF patents, which is really <a href="http://miningdrugs.blogspot.com/2007/07/osra-optical-structure-recognition.html">difficult and noisy</a>, I <a href="http://miningdrugs.blogspot.com/2007/04/publishing-chemical-picture-means-not.html">mean it</a>.</li><li>Third choice? Just get back to your <a href="http://en.wikipedia.org/wiki/Scoring_functions_for_docking">binding energy</a> modelling, <a href="http://en.wikipedia.org/wiki/Implicit_solvation">solvation</a> modelling, and <a href="http://en.wikipedia.org/wiki/Pharmacokinetics">PK modelling</a> and assume the structures are patentable. Under the <a href="http://miningdrugs.blogspot.com/2006/10/bounded-rational-drug-design.html">bounded rational drug design</a> paradigm is this statistically a reasonable approximation. But wait ! In contrast to statistics (where the average counts) is one patent enough to kill your lead series. ... o.k. ... now you can panic !</li></ol></div><div><b>See also</b><br /></div><div><ul><li>RSC/ChemSpider <a href="http://www.chemspider.com/blog/the-new-surechem-integration-unveiled-at-acs-washington.html">integrates SureChem</a> </li><li><a href="http://miningdrugs.blogspot.com/2009/01/collaboration-bullseye-20-information.html">information overload</a></li><li><a href="http://miningdrugs.blogspot.com/2009/01/collaboration-bullseye-20-information.html"></a><a href="http://miningdrugs.blogspot.com/2009/03/do-drug-innovation-while-information.html">drug innovation</a></li><li><a href="http://miningdrugs.blogspot.com/2009/03/do-drug-innovation-while-information.html"></a><a href="http://miningdrugs.blogspot.com/2006/10/bounded-rational-drug-design.html">(bounded) rational drug design</a></li></ul></div></div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-55363977750750906522009-08-15T19:49:00.008+02:002009-08-15T21:31:18.374+02:00The Web for Patients, Pets, and Scientists (Panel Discussion)(via <a href="http://usefulchem.blogspot.com/2009/08/making-web-work-for-science-july-28th.html">Jean-Claude Bradley</a>) <div>The panel discussion from <a href="http://en.wikipedia.org/wiki/Jimmy_Wales">Jimmy Wales</a> (founder of Wikipedia), <a href="http://en.wikipedia.org/wiki/John_Wilbanks">John Wilbanks</a> (VP Creative Commons), and Stephen Friend (founder of <a href="http://www.sagebase.org/">sage</a>) highlights a few examples of the web for scientists, pets, and patients.<div><ul><li><a href="http://www.dslrf.org/">Army of women</a> for breast cancer trials (driven by Susan Love)</li><li>Post-clinical trials, or patients sharing treatment details with each other - <a href="http://www.patientslikeme.com/">PatientsLikeMe</a></li><li><a href="http://petdiabetes.wikia.com/wiki/Main_Page">PetDiabetes</a> Wiki</li></ul><div>John Wilbanks made some really nice statements reflecting a deep understanding in the web and scientific world out there</div><div><ul><li>Actually, the scientific process is not so different from Wikis, in one you publish paper-by-paper, in Wikis you publish edit-by-edit. Though it might be a little slow and top-down.</li><li>In life sciences we have to be aware that we are talking about an evolved system (life), not a designed system (a chip), so never underestimate the role of human compilers processing information, in contrast to machine compilers processing information.<br />Comment JKW: I pretty much agree on this, and disagree with Stephen Friend, which mentioned that experts are overestimated.</li></ul></div><div>Finally, critical problems to solve are </div><div><ul><li>standardization, e.g. gene identifiers, chemical identifiers</li><li>stabilizing web-services, e.g. avoid change URLs, or provide redirects or schema backward compatibility</li><li>ensure stability and maintenance of services beyond funding periods</li><li>improve understanding of ambiguities, e.g. create semantics and ontologies </li></ul></div><br /><object width="400" height="270"><param name="allowfullscreen" value="true"><param name="allowscriptaccess" value="always"><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=6087817&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1"><embed src="http://vimeo.com/moogaloop.swf?clip_id=6087817&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="400" height="270"></embed></object><p><a href="http://vimeo.com/6087817">Making the Web Work for Science - Full</a> from <a href="http://vimeo.com/user510121">Jordan Mendelson</a> on <a href="http://vimeo.com/">Vimeo</a>.</p><br /></div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-72822904651567278552009-06-07T19:02:00.017+02:002009-06-07T22:22:35.321+02:00Google Wave - Mission Drug Design Federation<blockquote>"<span class="Apple-style-span" style="font-style: italic;">The Google Wave Federation Protocol may succeed email (an innovation from 1965), as the dominant form of Internet communication.</span>"<br />[<a href="http://en.wikipedia.org/wiki/Google_Wave_Federation_Protocol">Google Wave Federation Protocol @WP</a>]</blockquote>Google launched <a href="http://en.wikipedia.org/wiki/Google_Wave">Google Wave</a>. It is a mind-blowing <a href="http://mashable.com/2009/05/28/google-wave-guide/">technical platform</a>, which might just "change" <a href="http://davidhburton.com/author/blog//?p=1467">publishing</a>, <a href="http://scienceroll.com/2009/06/05/google-wave-in-science-and-medicine/">health support</a> of patients and physicians, and any other industry, where knowledge workers are suffering from <a href="http://kftf.ischool.washington.edu/index.htm">keeping found things found</a> (KFTF) and collaboration security (see <a href="http://friendfeed.com/sciphu/4bf7c857/on-challenges-of-conference-blogging-genetic">conference blogging</a>, <a href="http://friendfeed.com/science-2-0/00b2beed/message-to-nature-network-users-0-replies-via">libel law</a>, <a href="http://miningdrugs.blogspot.com/2009/05/we-know-that-scientific-collaboration.html">compliant commenting</a>, <a href="http://scienceroll.com/2008/03/15/dangers-of-web-20-in-medicine/">medicine 2.0 danger</a>). I do not think the GWave will replace collaboration tools, but it might enrich them, by facilitating information moderation and bridging (for all peers and channels).<div><br /></div><div>You can check first the Google Wave presentation (almost 1.5 hours), or continue reading below.<br /><div><br /><object height="344" width="425"><param name="movie" value="http://www.youtube.com/v/v_UyVmITiYQ&hl=de&fs=1&"><param name="allowFullScreen" value="true"><param name="allowscriptaccess" value="always"><embed src="http://www.youtube.com/v/v_UyVmITiYQ&hl=de&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="344" width="425"></embed></object><br /><br /></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="font-size:x-large;">What is the negative side?</span></span></div><div>There are two critical posts about GWave (<a href="http://ff.im/3ACGz">1</a>,<a href="http://friendfeed.com/google-wave/68417159/google-wave-doesn-t-look-like-tsunami-jungleg">2</a>), and I comment on them here.</div><div><ul><li><span class="Apple-style-span" style="font-weight: bold;">like instant messaging, an attention keeper</span>. I agree, but you could say the same for phone calls, meetings, or any other some2some, or some2many communication form. So, this can be easily disarmed by providing an "I am in the work-flow or busy" button, so do not expect immediate response. Just leave me alone and do not cause a workplace <a href="http://en.wikipedia.org/wiki/Distraction">distraction</a>.</li><li><span class="Apple-style-span" style="font-weight: bold;">instant typing and sentence rewriting is creepy</span>. I agree, it is like sitting in front of a washing machine, not really educational. There should be some degree of federation cache a user can trigger. Sometimes I might want to write even a full paragraph before getting viewed by others.</li><li><span class="Apple-style-span" style="font-weight: bold;">CCing wrong person.</span> This is a security leakage problem, and can happen with any electronic information. It is just a gut feeling, but I would assume that GWave could even trigger a recall or hold-back at any later stage. So, it might be even safer then the actual eMail system? Anyway, I still think that all confidential data should come with a <a href="http://oneswarm.cs.washington.edu/">peer2peer privacy</a> option, or any other form of encryption/decryption.</li><li><span class="Apple-style-span" style="font-weight: bold;">another silo of communication.</span> A what? If anything can bridge silos, then communication. The demo has shown that GWave can integrate already many other data silos, and it provides even an open communication layer. Thumbs up for Google for making the standard open.</li><li><span class="Apple-style-span" style="font-weight: bold;">user-wall gardening.</span> This is serious and opens again the question how many IDs a <a href="http://nsaunders.wordpress.com/2008/01/17/researcher-id/">researcher</a> can and should have nowadays. Why do you think are people talking about global IDs, like <a href="http://en.wikipedia.org/wiki/OpenID">OpenID</a>? Exactly, to get rid of all the many single logins. So, I rather trust Google then any other small startup for hosting my identity information. Though, any company with a lot of data has to take user data, especially patient data, serious, right <a href="http://friendfeed.com/silpol/820ca0f8/deny-this-last-fm">last.fm</a>? </li><li><span class="Apple-style-span" style="font-weight: bold;">eMail threads work, so why the Wave hype.</span> Honestly, I had already many2many threads with overlapping replies, and believe me, eMail fragmentation is a problem. At some point I was ending up with copying eMail parts to a word processor for allowing me to follow the argumentation sub-trees. And no, a live meeting is not an option, if people are in different (overlapping) meetings, buildings, and countries.</li></ul></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="font-size:x-large;">What is in there for drug design?</span></span></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="font-weight: normal;">The key feature is the federation of data and people sources, something like <a href="http://en.wikipedia.org/wiki/FriendFeed">FriendFeed</a> behind your company firewall in a secure legal environment. </span></span></div><div><span class="Apple-style-span" style="font-weight: bold;"><span class="Apple-style-span" style="font-weight: normal;"><blockquote>"<span class="Apple-style-span" style="font-style: italic;">@Google, please take data security very seriously, only a few people might want that confidential data is moving to your server. We can talk about <span class="Apple-style-span" style="font-weight: bold;">contribution tokens and embedding tools</span>, but data should stay in the remote company silo.</span>" [personal note]</blockquote></span></span></div><div><ul><li><span class="Apple-style-span" style="font-weight: bold;">Business Intelligence and News Alerts.</span> You might follow a series of business intelligence news, journal article news, or other news feeds. Is it not sometimes a pity, that the commenting happens all over the place? Sure, there are <a href="http://www.backtype.com/">BackType</a> and <a href="http://disqus.com/">Disqus</a> for a comment federation, but it would be so much nicer, if everything could be federated in one stream. The Google Wave demo showed a federation example with a blog post, so I assume this will be possible.</li><li><span class="Apple-style-span" style="font-weight: bold;">Dynamic Reporting.</span> Imagine you get an updated data report for your project X. As usual, people can reply via eMail and tell you what is nice or unexpected. But, it would be so much nicer, if people could actually collaborate on the data in one workflow, instead of switching forward and backward between different data sources and communication media. This could really boost efficiency.</li><li><span class="Apple-style-span" style="font-weight: bold;">Data Silo Bridging.</span> Like many other tools is the trend going towards peer and feed federation, like on FriendFeed, Yahoo pipes, or RSS readers. This are all tools with their own API. In other words, you will face the same communication problems you have with data warehouses, either you create all NxN relationships between the services, or communication will be inefficient. Why do you think have people invented <a href="http://www.biodas.org/wiki/Main_Page">BioDAS</a> or <a href="http://www.biomart.org/">BioMART</a>? Exactly, for having only one service many others can talk to, just like Google Wave. This will reduce the number of communication and API bridging efforts dramatically.</li><li><span class="Apple-style-span" style="font-weight: bold;">Project Feedback.</span> If I have a question within a project where the project members are not sitting in my room, my building, my campus, or even my country. What can I do? I write an eMail, and expect sometimes tree-like eMails threads, which are overlapping. If you like playing eMail puzzle, this might be fun, it is certainly not when you are having a busy work day. Then eMail fragmentation is a distraction. GWave looks promising and might just avoid this problem, totally.</li></ul></div><div>Finally, I think Google Wave can certainly reduce the information fragmentation and data silo bridging problem with its <a href="http://en.wikipedia.org/wiki/Google_Wave_Federation_Protocol">new and open federation protocol</a>.<br />I hope it might find its way into businesses with strict communication regulations, eg. Pharma, Medicine, or any other organization dealing with patient data. I further hope that Google takes <a href="http://miningdrugs.blogspot.com/2009/05/we-know-that-scientific-collaboration.html">data security</a> and <a href="http://en.wikipedia.org/wiki/Data_deduplication">data duplication</a> issues very seriously in their federation protocol. Google might have here an ability to tackle both things, I am looking forward to it.</div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com4tag:blogger.com,1999:blog-26255983.post-28425566217719007282009-05-30T00:09:00.010+02:002009-05-30T00:47:19.142+02:00Drug popularity (via Google queries) - Yet Another Long Tail (YALT)Here some drug popularity trends based on automatic Google queries. The drug names were taken from <a href="http://www.drugbank.ca/">DrugBank</a>.<script type="text/javascript" src="http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/23abd28a4c9d11debe2e000255111976/comments/23b04ed24c9d11debe2e000255111976.js?width=400&height=350"></script><script type="text/javascript" src="http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/e4adb3664c9a11dea898000255111976/comments/e4b947444c9a11dea898000255111976.js?width=400&height=350"></script><br /><div><span style="font-weight:bold;">The top ten are</span><br /><ol><li>Cholesterol<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=5775&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Aspirin<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=2157&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Ethanol<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=682&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Ibuprofen<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=3544&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li><a href="http://en.wikipedia.org/wiki/Insulin">Insulin</a><br></br><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibIKsqRZiaVVlb7pRdYSA6yDy2ImsSOSDjSi5fQ-HU9ph42XxJf0c1AmyiWRIKgmk_P21Ufc5soTAN1L7P1kpuJbkVhd7E54O4Y0uiyH0QnKCQAEZq51-RjR58gXyghFyGu_kD/s1600-h/250px-InsulinHexamer.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 250px; height: 170px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibIKsqRZiaVVlb7pRdYSA6yDy2ImsSOSDjSi5fQ-HU9ph42XxJf0c1AmyiWRIKgmk_P21Ufc5soTAN1L7P1kpuJbkVhd7E54O4Y0uiyH0QnKCQAEZq51-RjR58gXyghFyGu_kD/s320/250px-InsulinHexamer.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5341378440441556178" /></a><br /></li><li>Acetaminophen<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=1906&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Testosterone<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=5791&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Cocaine<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=10194104&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Oxycodone<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=4447649&w=150&eid=Drug+popularity+2009-05+(top+10)"></script><br /></li><li>Vardenafil<br></br><script type="text/javascript" src="http://www.chemspider.com/csjsapi.ashx?op=img&tk=a1ef575b-ce61-449f-89b6-b3c88e2dc295&id=99300&w=150&eid=Drug+popularity+2009-05+(top+10)"></script></li></ol><br /><span class="Apple-style-span" style="font-weight: bold;">References</span><ul><li>I used a Python script for the Google data fetching. Let me know, if you need more details.</li><li>The Long Tail <a href="http://en.wikipedia.org/wiki/The_Long_Tail">@Wikipedia</a></li><li><span class="Apple-style-span" style="font-style: italic;">DrugBank: a knowledgebase for drugs, drug actions and drug targets. </span><br />Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M.<br />Nucleic Acids Res. <span class="Apple-style-span" style="font-weight: bold;">2008, </span>36, (Database issue):D901-6.<br />PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/18048412">18048412</a><br /></li><li><span class="Apple-style-span" style="font-style: italic;">DrugBank: a comprehensive resource for in silico drug discovery and exploration.</span><br />Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J.<br />Nucleic Acids Res. <span class="Apple-style-span" style="font-weight: bold;">2006, </span>34, (Database issue):D668-72. <br />PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/16381955">16381955</a></li></ul></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com2tag:blogger.com,1999:blog-26255983.post-51057322818163762872009-05-26T22:18:00.008+02:002009-05-26T22:52:42.260+02:00Compliant commenting in science 2.0We know that <a href="http://www.nature.com/news/2009/090318/full/458274a.html">scientific collaboration</a> is important, but what is holding people back to contribute to web 2.0 communities (of people, like you!) ?<br />This <a href="http://friendfeed.com/science-2-0/9af350c1/why-people-do-not-comment-online-articles-what">question was raised on FriendFeed</a> (another web 2.0 platform, a good one). <br /><br />Though I answered parts of this <a href="http://miningdrugs.blogspot.com/2006/09/even-if-online-what-is-missing-for.html">question earlier</a>, here a focus on the increasing number of compliance regulations, especially for people in industry (e.g. drug design). Beside, please check also the <a href="http://scienceroll.com/2008/03/15/dangers-of-web-20-in-medicine/">dangers in health/medicine 2.0</a>.<br /><div style="width:425px;text-align:left" id="__ss_1491990"><a style="font:14px Helvetica,Arial,Sans-serif;display:block;margin:12px 0 3px 0;text-decoration:underline;" href="http://www.slideshare.net/joergkurtwegner/science-and-compliant-commenting?type=powerpoint" title="Science And Compliant Commenting">Science And Compliant Commenting</a><object style="margin:0px" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=scienceandcompliantcommenting-090526150607-phpapp02&stripped_title=science-and-compliant-commenting"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=scienceandcompliantcommenting-090526150607-phpapp02&stripped_title=science-and-compliant-commenting" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="font-size:11px;font-family:tahoma,arial;height:26px;padding-top:2px;">View more <a style="text-decoration:underline;" href="http://www.slideshare.net/">OpenOffice presentations</a> from <a style="text-decoration:underline;" href="http://www.slideshare.net/joergkurtwegner">Joerg kurt Wegner</a>.</div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-50959450216304440622009-05-19T21:16:00.012+02:002009-05-19T22:53:57.982+02:00Peer recognition and building relationships - Even in drug design<blockquote>"<span style="font-style: italic;">Experts will want to contribute to coworkers who need them, who will hear them, who will respect them and who may even thank them. ... Rather than asking, How do we incentivise people to share their knowledge? It would be more useful to ask, How do we develop relationships across the globe that will set in motion more knowledge sharing?</span>" [slightly generalized after <a href="http://www.nancydixonblog.com/2009/03/the-incentive-question-or-why-people-share-knowledge.html">Nancy Dixon</a>]</blockquote><blockquote>"<span style="font-style: italic;">Today there seems to be a new distribution model that is emerging. One that is based on people’s ability to publically syndicate and distribute messages — aka content — in an open manner. This has been a part of the internet since day one — yet now its emerging in a different form — it's not pages, it's streams, its social and so its syndication.</span>" [<a href="http://www.businessinsider.com/henry-blodget-the-rise-of-social-distribution-networks-2009-5">John Borthwick</a>]</blockquote>Recently, there are many efforts ongoing to build relationships in the drug design community, and yes, the peers are recognizing and appreciating those efforts.<br /><ul><li>WikiChemists and Chemical Abstract Service (CAS) announced their <a href="http://en.wikipedia.org/wiki/Wikipedia:Wikipedia_Signpost/2009-05-18/Chemistry_data">collaboration</a>. Beside, we should never forget that this is a community achievement of many people, especially the <a href="http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Chemistry">WikiChemists</a> and everybody involved in <a href="http://www.chemspider.com/blog/the-royal-society-of-chemistry-acquires-chemspider.html">ChemSpider (appreciated by RSC</a>). Dear CAS, we appreciate, that <a href="http://pubs.acs.org/cen/email/html/cen_87_i20_8720notw3.html">you appreciate</a>.</li><li><a href="http://www.chemspider.com/blog/welcome-chemmantis-to-chemzoo-and-a-call-for-contributions-to-the-community.html">ChemMantis</a> (<a href="http://www.slideshare.net/AntonyWilliams/crowdsourcing-collaborations-and-textmining-in-a-world-of-open-chemistry-1366224">slides</a>) and <a href="http://www.elseviergrandchallenge.com/team1.html">Reflect</a> (<a href="http://www.elseviergrandchallenge.com/webcast_reflect.html">webcast</a>) bridge chemical and biological data silos. This saves time and enriches information and is peer appreciated.<br /></li><li><a href="http://biskit.pasteur.fr/">Biskit</a> bridges tools and services manipulating and analyzing macromolecular structures, protein complexes, and molecular dynamics trajectories. If you ask me, any efforts making daily life easier and giving access to many tools via one interface is peer appreciated.</li><li><a href="http://www.citeulike.org/user/joergkurtwegner/article/4488840">BioMart</a> and <a href="http://www.citeulike.org/user/joergkurtwegner/article/3064678">DAS</a> (Distributed Annotation System) are both systems designed for accessing many biological data sources via a unified interface. This is peer appreciated.<br /></li><li>The <a href="http://www.citeulike.org/user/joergkurtwegner/article/1756058">Functional Genomics Experiment</a> data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. The community is<a href="http://www.citeulike.org/user/joergkurtwegner/article/4540763"> using it and contributes</a> to the development of convergent data standards in omics research. Clearly, peer appreciated.<br /></li><li>When thinking about drug or side-effect re-use, a lot of information and people were involved in creating this information. So, helping patients by bringing drugs to people to drugs to people to ... is peer appreciated.<br /><div style="width: 425px; text-align: left;" id="__ss_1457222"><a style="margin: 12px 0pt 3px; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; display: block; text-decoration: underline;" href="http://www.slideshare.net/larsjuhljensen/predicting-novel-targets-for-existing-drugs-using-side-effect-information?type=powerpoint" title="Predicting novel targets for existing drugs using side effect information">Predicting novel targets for existing drugs using side effect information</a></div></li></ul><object style="margin: 0px;" height="355" width="425"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=jen09talk8-090519041113-phpapp01&stripped_title=predicting-novel-targets-for-existing-drugs-using-side-effect-information"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=jen09talk8-090519041113-phpapp01&stripped_title=predicting-novel-targets-for-existing-drugs-using-side-effect-information" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="355" width="425"></embed></object>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-38159361860822716112009-05-11T20:44:00.001+02:002009-05-11T20:53:53.663+02:00Tag cloud - Mining Drug Space - May 2009<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVCWyY7P2h4MjD4_eRSXzDx4oS41JVYsP2LJ4SAdf-37tbc8RjO40guUC65Y89FsU7-aqEkobwU2gxiFmJV8IVhTpSFxkqCoafifLrvFzwGaEcQIjMrmHFiJbRYRF7YS2vPnlG/s1600-h/wordle_mds_2009_05_11.gif"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 166px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVCWyY7P2h4MjD4_eRSXzDx4oS41JVYsP2LJ4SAdf-37tbc8RjO40guUC65Y89FsU7-aqEkobwU2gxiFmJV8IVhTpSFxkqCoafifLrvFzwGaEcQIjMrmHFiJbRYRF7YS2vPnlG/s400/wordle_mds_2009_05_11.gif" border="0" alt="" id="BLOGGER_PHOTO_ID_5334641080094013906" /></a>As created by <a href="http://www.wordle.net/gallery/wrdl/836260/Mining_Drug_Space_2009-05">Wordle</a>.Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com0tag:blogger.com,1999:blog-26255983.post-48997540155538437512009-05-06T20:32:00.015+02:002009-05-09T17:38:15.980+02:00Drug design and thinking the unthinkable<blockquote>"<span class="Apple-style-span" style="font-style: italic;">The problem pharma industry faces isn’t that they didn’t see generics coming. They not only saw it miles off, they figured out early on that they needed a plan to deal with it. ... In drug design the unthinkable scenario unfolded something like this: The ability to share data and intellectual properties wouldn’t shrink, it would grow. Walled data silos would prove unpopular and inefficient. ... No one experiment is going to replace what we are now losing with designed drugs, but over time, the collection of new experiments that do work might give us the cure we need.</span>" [adapted from <a href="http://www.shirky.com/weblog/2009/03/newspapers-and-thinking-the-unthinkable/">Clay Shirky</a>]</blockquote><div><div>We need legal support, intellectual property protection, and social legal systems, we need them more than ever ! Sure, we want to work 'openly' together, but not without payment. I think there are little intentions of patients and scientists to starve themselves to death for providing a health benefit to others. The key question is therefore how we can measure knowledge and contributions allowing us to reward the support of patients and scientists? Is there any metric or legal system we can adapt? If you have any idea, let me know !</div><div><blockquote>"<span class="Apple-style-span" style="font-style: italic;">You can’t control what you can't measure.</span>" [<a href="http://en.wikipedia.org/wiki/Software_metric">Tom DeMarco</a>]</blockquote></div><div>What can we learn from</div><div><ul><li><a href="http://en.wikipedia.org/wiki/Lawrence_Lessig">Lawrence Lessing</a> (legal aspects of free cultures), </li><li><a href="http://andrewmcafee.org/blog/?page_id=546">Andrew McAfee</a> (Enterprise 2.0), and the</li><li><a href="http://dotank.nyls.edu/Aboutus.html">Do Tank</a> for delivering <a href="http://miningdrugs.blogspot.com/2009/03/do-drug-innovation-while-information.html">Do Drug Development (D<sup>3</sup>) solutions</a> </li></ul></div></div><br /><div style="text-align: center;"><span class="Apple-style-span" style="color: rgb(0, 0, 238); text-decoration: underline;"><br /></span></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com1tag:blogger.com,1999:blog-26255983.post-23336449438852035302009-03-30T19:30:00.017+02:002009-03-30T21:20:42.376+02:00Open innovation in drug design? - I do not think so!Triggered by <a href="http://friendfeed.com/e/b4adf06c-39b4-a8b3-0c06-4247ab2c2e06/Walking-the-walk-The-practical-experience-of-Web2/">slides and a discussion</a> from Cameron Neylon was I wondering, to which degree people believe in open innovation for the drug design community?<div>Though the principle seems valid for a few software companies, is there little support for life sciences on this topic.</div><blockquote>"<span class="Apple-style-span" style="font-style: italic;">It's an area that's just not been explored much. The usual flow is very much linear. Can be developed in academia, is then licensed via tech transfer.</span>" [<a href="http://friendfeed.com/e/b4adf06c-39b4-a8b3-0c06-4247ab2c2e06/Walking-the-walk-The-practical-experience-of-Web2/">Deepak</a>]</blockquote><blockquote>"<span class="Apple-style-span" style="font-style: italic;">The question is whether a business can make money by a route that doesn't involve patents (or copyright). There are examples of that, O'Reilly publishing being the most obvious but they are pretty thin.</span>" [<a href="http://friendfeed.com/e/b4adf06c-39b4-a8b3-0c06-4247ab2c2e06/Walking-the-walk-The-practical-experience-of-Web2/">Cameron</a>]</blockquote>In other words, if you do not need the money, do whatever you like openly. <div>If you need the money, e.g. for clinical trials, then please make sure staying within the same legal framework, which is most probably not open! Do not misunderstand this, I still strongly believe in (the legally encapsulated) web 2.0 !<br /></div><div><br /></div><div><span class="Apple-style-span" style="font-weight: bold;">Drug design is not like the IT industry</span></div><div><span class="Apple-style-span" style="font-weight: bold;"><br /></span></div><div>Some people think drug design is like chip or software design, e.g. by (over)simplifying the business models. I heard that before, and I still <a href="http://miningdrugs.blogspot.com/2007/11/andy-grove-when-silicon-indoctrinates.html">doubt so</a>! Chip and software design are mostly an engineering task of known facts or an optimization of measurable parameters. In contrast, drug design uses often facts or parameters from the <a href="http://dx.doi.org/10.1093/bfgp/eln033">tip of the iceberg</a>, but there are <a href="http://miningdrugs.blogspot.com/2006/10/bounded-rational-drug-design.html">much more unknowns</a> , or even things we can not look at (like <a href="http://en.wikipedia.org/wiki/Metabolic_pathway">*all* metabolic pathways</a> in humans)! Beside, the <a href="http://www.1000genomes.org/">exploding</a> amount of information is <a href="http://miningdrugs.blogspot.com/2009/03/do-drug-innovation-while-information.html">making things not easier</a>.<br /><br />On the other hand, who could blame humans for oversimplifying problems ...<br /></div><div></div><blockquote><div><span class="Apple-style-span" style="font-style: italic;">Unless we concentrate very hard, we often simplify a problem, because our minds routinely do so without knowing it.<br /></span></div><div><span class="Apple-style-span" style="font-style: italic;">Many people confuse the statement that "almost all drugs are small molecules" with "almost all small molecules are drugs". Assume that the first statement is true, that 96 percent of drugs are small molecules (not counting biotech, or nutraceutical drugs). This would mean that only about 0.01 percent of small molecules are drugs, since there are more than</span><span class="Apple-style-span" style="font-style: italic;"> 24 million </span><span class="Apple-style-span" style="font-style: italic;">physically existing </span><span class="Apple-style-span" style="font-style: italic;">small molecules and only 4600 drugs, roughly one in five thousand. So the logical mistake makes you (unconsciously) overestimate the odds of a randomly drawn small molecule being a drug by more than five thousand times !</span> [freely adapted after <a href="http://en.wikipedia.org/wiki/The_Black_Swan_%28Taleb_book%29">The Black Swan, p 52</a>]</div></blockquote><span class="Apple-style-span" style="font-weight: bold;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://upload.wikimedia.org/wikipedia/en/1/17/The_black_swan_taleb_cover.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 200px; height: 200px;" src="http://upload.wikimedia.org/wikipedia/en/1/17/The_black_swan_taleb_cover.jpg" alt="" border="0" /></a>References</span><br /><ul><li>4637 small molecule, 137 biotech, and nutraceutical drugs as taken from <a href="http://www.drugbank.ca/stats">DrugBank 2009-03</a>. The number of 24 millions physically existing (as published, not as existing or purchaseable) small molecules was taken from a recent <a href="http://dx.doi.org/10.1021/jo8001276">CAS publication</a>.<br /></li></ul>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com5tag:blogger.com,1999:blog-26255983.post-17426974581658566452009-03-26T21:23:00.011+01:002009-03-26T22:01:40.133+01:00The future of science and scientists - walking into open innovation ?<blockquote>"<span class="Apple-style-span" style="font-style: italic;">If you just build it they (probably) won’t come...<br />If you don’t build it they definitely won’t come...<br />The community is more important than the service...<br />Researchers are already the tail !</span>" [<a href="http://www.slideshare.net/CameronNeylon/walking-the-walk-the-practical-experience-of-web2-in-research-1201087">Cameron Neylon</a>]<br /></blockquote><blockquote>"<span class="Apple-style-span" style="font-style: italic;">An ideal collaboration market will enable just such an exchange of questions and ideas. It will bake in metrics of contribution so participants can demonstrate the impact their work is having. Contributions will be archived, timestamped, and signed, so it’s clear who said what, and when. Combined with high quality filtering and search tools, the result will be an open culture of trust which gives scientists a real incentive to outsource problems, and contribute in areas where they have a great comparative advantage. This will change science.</span>" [<a href="http://michaelnielsen.org/blog/?p=448">Michael Nielsen</a>]<br /></blockquote><blockquote>"<span class="Apple-style-span" style="font-style: italic;">Specialization will be one of many factors influencing creation of new types of scientists. And what are these types? Let me describe a few.</span>" [<a href="http://freelancingscience.com/2009/03/26/the-future-of-life-scientists/">Pawel Szczesny</a>]<br /></blockquote><div style="width:425px;text-align:left" id="__ss_1201087"><a style="font:14px Helvetica,Arial,Sans-serif;display:block;margin:12px 0 3px 0;text-decoration:underline;" href="http://www.slideshare.net/CameronNeylon/walking-the-walk-the-practical-experience-of-web2-in-research-1201087?type=presentation" title="Walking the walk - the practical experience of Web2 in research">Walking the walk - the practical experience of Web2 in research</a><object style="margin:0px" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=userscamerondocumentsaa-isisdocspresentationsscience2-0esiweb2workshop-090326050843-phpapp01&stripped_title=walking-the-walk-the-practical-experience-of-web2-in-research-1201087"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=userscamerondocumentsaa-isisdocspresentationsscience2-0esiweb2workshop-090326050843-phpapp01&stripped_title=walking-the-walk-the-practical-experience-of-web2-in-research-1201087" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="font-size:11px;font-family:tahoma,arial;height:26px;padding-top:2px;">View more <a style="text-decoration:underline;" href="http://www.slideshare.net/">presentations</a> from <a style="text-decoration:underline;" href="http://www.slideshare.net/CameronNeylon">CameronNeylon</a>.</div></div><div style="width:425px;text-align:left" id="__ss_1201945"><a style="font:14px Helvetica,Arial,Sans-serif;display:block;margin:12px 0 3px 0;text-decoration:underline;" href="http://www.slideshare.net/wilbanks/etech-wilbanks?type=powerpoint" title="Etech Wilbanks">Etech Wilbanks</a> via <a href="http://scienceblogs.com/commonknowledge/2009/03/lions_tigers_and_crowds.php">common knowledge</a>, Lions, Tigers, Crowds<object style="margin:0px" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=etechwilbanks-090326074611-phpapp01&stripped_title=etech-wilbanks"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=etechwilbanks-090326074611-phpapp01&stripped_title=etech-wilbanks" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="font-size:11px;font-family:tahoma,arial;height:26px;padding-top:2px;">View more <a style="text-decoration:underline;" href="http://www.slideshare.net/">presentations</a> from <a style="text-decoration:underline;" href="http://www.slideshare.net/wilbanks">John Wilbanks</a>.</div></div>Anonymoushttp://www.blogger.com/profile/09112376168632883058noreply@blogger.com4