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The Wonderful World of Wikis for Life Scientists

Posted by Mary Canady June 14th, 2010 .
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life science social media resource

You may know that the San Diego Biotechnology Network, and its partner company, Comprendia, are dedicated to improving communication between life scientists and the companies that serve them. As part of this objective, we like to pass on resources for both groups to help, check out our video resources for life science and the list of life science companies using social media. Life scientists can use the wiki list below as a reference and to learn and contribute, and companies should realize the potential that resources such as these present for helping their customers put the complex science behind their products in context.

What is a wiki? Many use the term loosely these days, to refer to any web resource. To us, a wiki is a community-driven, content rich website in which many of the pages are interconnected. There are many free software programs to generate wikis, and even a resource which lists wikis and helps you choose which one will best meet your needs.

We’ve been looking into life science wikis, and with help from the Life Scientists group on Friendfeed, came up with the list below. There are a few schools of thought on wikis. Some believe that all content should reside on Wikipedia (only two Wikipedia-based wikis are listed below). Others feel as though wikis specific for life science, outside of wikipedia, offer a more targeted approach. Also, some feel as though they must remain ‘pure’ and have no advertising. However, these wikis require a lot of work, I see no problem with this as long as the companies are transparent with their association with the resource, and are careful to not turn it into solely self-serving.

There is an enormous potential for life science companies to leverage wikis. Why not a signal transduction wiki sponsored by the companies who sell products in that area (in fact, there is a defunct cell signaling portal on Wikipedia which could be rescued)? Enzyme classes, areas of study (e.g. stem cells), disease areas…the possibilities are limitless! See German distributor Biomol’s wiki–they’ve created a wiki-based product listing supplemented with supporting biological information (p.s. search engines love wikis, perhaps for this reason). We see some life science companies creating fancy flash animations to highlight their products…guess what, search engines cannot see the content in flash! In addition, scientists are accustomed to wikis, there is no need to reinvent the wheel with a fancy new application, something we’ve discussed on the Comprendia blog.

If you represent a life science company who would like to learn how to leverage wikis, attend Comprendia’s Social Media for Life Science and Biotechnology Workshop in San Diego June 22nd, where we’ll cover the Basics, Benefits, Best Practices, and Biotech Examples. Don’t live in San Diego? Contact Comprendia to learn about virtual workshops or visits to your area.

Life Science Wikis

Wiki Subject Contributors Sponsors Details
ACS Chemical Biology Community Chemical biology Life scientists ACS A bit confusing because it does not have the standard wiki interface. Hard to tell if it is active.
Biomol Wiki Life science research products Life science companies Biomol GmBH Interesting mix of life science and products. Biomol is a distributor of products from life science vendors, and has created an extensive wiki for their products.
ChemWiki Chemistry Anyone/editors curate UC Davis Chemistry textbook–lots of content.
EcoliWiki All things E. coli Life scientists, with auto-generated content Part of EcoliHub, NIH/NIGMS (Purdue, Oklahoma, SRI, TAMU) Very impressive source of information about genes, proteins, expression levels.
Encyclopedia of Life Biology Anyone/editors curate Harvard University, the Field Museum of Natural
History, the Marine Biological Laboratory, the Smithsonian Institution, the Biodiversity Heritage Library,
and the Missouri Botanical Garden. Funding: John D. and Catherine T.
MacArthur Foundation and the
Alfred P. Sloan Foundation
Collaboration between scientific community and the public. Goal is to disseminate knowledge about the world’s organisms.
Medpedia Health and medicine M.D.’s and Ph.D.’s Harvard, Stanford, UC Berkeley, University of Michigan Nice resource. All content generated by M.D.’s and Ph.D.’s, and each entry has a ‘clinical’ and ‘plain english’ description. Users can ask questions to the editors.
MicrobeWiki Microbiology Life scientists Kenyon College Mostly class material-centric, nicely done with a lot of images.
OpenWetWare Life science laboratories, protocols, and classes Life scientists Individual labs at MIT (NSF grant submitted) Very interesting and popular site. Several different types of entries. Labs can create their own site here to enter their schedules, presentations, and protocols. Class materials can also be organized here.
Protopedia Structural biology Structural biologists, with a large amount of auto-generated content Weizmann Institute, The Israel Structural Proteomics Center Very nicely done–they have created pages for every entry in the protein data bank.
SciTopics General science Scientists Elsevier May be a bit too general for life scientists.
SNPedia SNPs (single nucleotide polymorphisms) Life scientists Independent–started by Michael Cariaso. Catalog of more than 11,000 SNPs. Shows SNPs related to interesting phenotypes such as "sprinting versus endurance muscles." SNPs are downloadable, and there is also a page dedicated to getting your personal SNPs identified.
Subtiwiki All things B. subtilis Life scientists, with auto-generated content University of Gottingen Similar to EcoliWiki.
TOPSAN Structural biology Structural biologists ? “The Open Protein Structure Annotation Network” focusing on sharing information about protein structures determined by structural genomics efforts.
WikiGenes Genes, proteins, chemical compounds, diseases Life scientists Society in Science – The Branco Weiss Fellowship. Original paper published by Robert Hoffmann at MIT. Contains a lot of useful information. Tracks authors of every contribution and allows rating of contributions.
Wikimedia Commons Biology, chemistry sections Anyone Wikimedia foundation May be too general for most life scientists. Focuses on media for download (e.g., images, sound).
Wikipedia: WikiProject Gene Wiki Genes and function Anyone/editors curate NIH/GNF A portal which helps to organize and update entries in Wikipedia involving gene and protein function.
Wikipedia: WikiProject Molecular and Cellular Biology Molecular and cell biology Anyone/editors curate ? A portal which helps to organize and update entries in Wikipedia involving molecular and cell biology. Appears to be stagnant at this point.
Wikispecies Biological species Biologists Wikimedia Foundation May be too general for life scientists.

What are your opinions about these ‘free standing’ wikis, outside of wikipedia? Is the redundance found on the wikis troubling, are these private efforts confusing and contrary to the objectives of NCBI, RCSB, etc.? Also, how would you feel if life science companies started to sponsor more wikis? Leave a comment below, and let the discussion begin!

To share easily, cut and paste: The Wonderful World of Wikis for Life Scientists http://bit.ly/apZTOs

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Jon Eisen – Genomic Encyclopedia of Bacteria and Archaea to sample the breadth of microbial diversity

Posted by Dr. Gunn May 28th, 2010 .
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@phylogenomics, @rnaworld, and @comprendia discussing deep scientific matters at the ASM tweetupI recently attended the 2010 American Society for Microbiology General Meeting with my colleague Mary Canady. I’ll be covered the scientific sessions and shared interesting developments in genetics, microbiology, and technology. See also the #ASMGM hashtag on twitter for conference tweets.

Jonathan Eisen spoke Tuesday on the Genomic Encyclopedia of Bacteria and Archaea, an ambitious project to sample across the breadth of microbial diversity and get a sense of just how much genetic diversity is represented across all bacteria. This project was undertaken to get a more balanced picture of genetic diversity, which is currently skewed in modern sequencing projects by under-representation of some groups. Genome sequence data has diverse uses including development of new antibiotics and drugs, as well as for the identification of new species, but without a big picture overview of the “Tree of Life“, scientists are very much like tourists in a strange city without a map, only finding the interesting stuff if they happen to stumble upon it. (more…)

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Stephen Quake Keynote: Single-molecule sequencing shows microbial diversity is greater than expected #ASMGM

Posted by Dr. Gunn May 26th, 2010 .
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I’m blogging this week from the 2010 American Society for Microbiology General Meeting with my colleague Mary Canady. I’ll be covering the scientific sessions and sharing interesting developments in genetics, microbiology, and technology. You can also follow the #ASMGM hashtag on twitter for updates.

Sunday night kicked off the conference with a presentation from Stanford bioengineering professor Dr. Stephen Quake, founder of Helicos Biosciences. Dr. Quake attained a mild amount of fame for being the first person to sequence his own genome, as opposed to the multi-center effort that went into the Human Genome Project.

Dr. Quake’s company Helicos has dramatically reduced the time and cost for sequencing projects, broadly expanding the application reach of sequencing. Faster, cheaper sequencing puts genomes within the grasp of smaller research groups, so it’s no surprise that microbiologists have begun to use it to sequence their favorite subjects.

Because the Helicos instrument is so sensitive, it can actually get a sequence from as little as a single cell, so biologists have begun to sample the “sequence space” of interesting microbiological habitats. One such habitat is the termite gut. Termites have the unique ability to digest wood due to microorganisms resident in their gut, but what Dr. Quake’s collaborators found is that it’s not just one species, but as many as 13 species are present, based on sequences recovered from gut samples. Knowledge of the different species living in this habitat can be used to develop new termite-resistant building materials, but just the fact that 13 different species are found in the gut of this tiny little creature was enough to impress the crowd here. Even more interestingly, it seems that the functions of the microbes are non-overlapping, so it’s no accident all these species are there, rather they serve as a form of evolutionary insurance for the termite. Even though one species would have been enough, having multiple species allows the termite to survive habitat changes that might have been less compatible with the resident bacteria.

As with the sequencing of his own genome, the technical details behind this effort are likewise fascinating (if you ask me, the engineering details nearly put those next to me to sleep). The key advance to make the sequencing work is the applicability of the technique to very small samples, such as you might be forced to work with if you wanted to study a bacteria found in nature that no one has yet learned how to cultivate in the lab. To work with samples in the nanoliter range, they developed an ingenious tiny valve controlled by overlapping expandable microchannels. Inflating one set of tubes would expand the wall into the adjacent tube, shutting of the flow of the adjacent channel. Printing complex patterns via lithography allowed them to sample, mix, and separate volumes small enough to contain a single bacterium. Next, they had to solve the problem of off rates, which are a fundamental limitation to how miniaturized an assay can be. They solved this by using a clear polymer to trap the solution over the assay surface, vastly reducing the volume into which the dye could diffuse.

Speaking before Dr. Quake was Yoshi Kawaoka, describing the synthesis of 1918 flu in the lab, technical advancement that aids the study of modern pandemic flu by comparison with this older, more deadly strain. Further work by Dr. Kawaoka led to the development of a novel neuraminidase inhibitor with activity against pandemic H1N1.

[Disclosures: Dr. Gunn is a San Diego-based scientific consultant and academic community liaison for Mendeley. Former clients include a private single molecule sequencing startup.]

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Flip This Asset: San Diego’s Advanced BioHealing ‘Fixed Up’ Dermagraft for Profit and Growth #BIO2010

Posted by Mary Canady May 5th, 2010 .
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bio_conf-logo1-300x218_2Wednesday I attended a regenerative medicine-focused breakfast at the BIO convention and learned about San Diego company Advanced BioHealing (ABH), who took a ‘fallen’ asset, Dermagraft, and not only turned it into an $85M/year product, but is also looking for new indications. Dermagraft was sold by Advanced Tissue Sciences, who had invested hundreds of millions into developing it, and even got FDA approval for the product to treat diabetic foot ulcers.
I spoke with Advanced BioHealing’s Senior VP Dean Tozer, and he describes their methodology as ‘reverse biotech,’ meaning that they first focused on commercializing products, and just recently hired their CSO Charles Hart. Hart will be spearheading the efforts to find soft tissue indications for Dermagraft. This is counter to how most biotechs in San Diego form, and it appears to be working for ABH as they are predicting 30-50% growth over the next few years.
This growth translates to jobs in San Diego, with 15 listed on the ABH careers page currently. ABH has locations in Westport, Connecticut and Nashville, Tennessee as well, and plans to continue manufacturing products in their 70,000 square foot La Jolla site near the Burnham Institute, and has recently acquired 20,000 square feet of office space nearby in an old Pfizer site. I asked Tozer whether the jobs will continue to be created in San Diego, and he said yes, because the talent pool here is so valuable to them.
What can other San Diego biotechs learn from this example? At BIO this year, I have seen successful repurposing of assets and information. It may simply be the product of a down economy, but I wonder what we can learn, and what could be gained by investigating failed assets that exist from local companies who have not survived? Tozer also believes strongly that the right people make the difference, and they were lucky to bring together a team which understands biotech commercialization. Surely, attracting or training more commercially focused professionals in the area would be a great start.

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How Does Biomarker Stratification Affect Drug Development Cost? It Depends. #BIO2010

Posted by Mary Canady May 5th, 2010 .
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bio_conf-logo1-300x218_2On the San Diego Biotechnology Network LinkedIn group, we asked you what you wanted to hear about from the BIO Convention in Chicago, and you requested to hear about Biomarkers. Tuesday I attended a breakout session titled ‘Impact of Biomarkers on Drug Development Complexity and Cost,’ and it described a study done by panel members Federico Goodsaid of the FDA, Michael Palmer of Adaptive Pharmacogenomics, Mark Trusheim of MIT, Steven Averbuch of BMS, Theresa Long of the Van Andel Institute. The study modeled different scenarios utilizing biomarker information and the financial impact on estimated net present value (eNPV) of developed drugs. The group was truly interdisciplinary, and it was clear from the quality of the presentations that they likely worked well together due to their communication skills.
The session described a workshop held in October of 2009 in which case studies on oncology and alzheimers were discussed (featured in Nature Reviews Drug Discovery as well–requires login).
MIT economist Mark Trusheim began by describing the ‘pharmaeconomics’ of choosing patient populations for clinical trials. There are obvious benefits to using biomarkers to enrich populations, but there are many factors which need to be considered, and ultimately it depends on the science behind the drug and the market. The group determined three factors to be the most important: variability in the therapeutic effectiveness of the drug, prevalence of the biomarker, and the quality of companion diagnostics. Trusheim also described modeling different long term scenarios ranging from Phase II extending through to the end of market exclusivity, from the perfect ‘Nirvana’ situation, where everything goes perfectly, to ‘pharmageddon’ where it goes bad at every turn. Trusheim indicated that in both the oncology and Alzheimer’s study, a very significant increase in eNPV could be achieved by utilizing biomarker information.
Steven Averbuch, VP of Oncology at BMS, covered the study results for Herceptin and Vectibix for oncology indications. In the case of Herceptin, it had a large effect on a small population, saving money and adding to the eNPV by allowing a smaller clinical trial, but perhaps precluding the discovery of other biomarkers or indications for the drug, as was found to be important for drugs such as Gleevec. Vectibix had a large effect on a large population, obviating the need for biomarker stratification but giving the drug a higher eNPV because of a larger market size. Averbuch reiterated Trusheim’s three important factors, and the need for increased communication between all the stakeholders to utilize biomarker information to help move from the ‘pharmageddon’ to nirvana drug development situation.
Theresa Long, presented the study on the Alzheimer’s drug Bapineuzumab, and the effect of biomarker stratification on a chronic condition. They used the ApoE4 biomarker and started with data past Phase 2. Three different scenarios were modeled, from an all-inclusive to stratified, with an 80% increase in eNPV in the biomarker study. Long stressed the importance of knowing the prevalence of the biomarker in the population, even for chronic conditions such as Alzheimer’s which has blockbuster potential.
This session was inspiring as it showed how science can drive drug development and how biomarker stratification could lead pharma and healthcare towards a path of increased communication resulting in lower costs. The study has been submitted for publication and the modeling tools that were used will be available. Federico Goodsaid indicated that the tool could be made available to those who contact him.

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