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Speaking of pipelines, what about the education pipeline? #oss2010

Posted by Dr. Gunn August 3rd, 2010 .
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This is a post from the Open Science Summit, a weekend of talks and discussion about this emerging research approach. Disclosure: Mendeley Research Networks is a sponsor of OSS2010.

Friday had a short series of talks on applying microfinance and crowdfunding models to doing science. David Vitrant from Fund Science, David Fries from SciFlies, and Jason Blue Smith from EurekaFund spoke in this session. The idea behind microfinance is to provide a alternative channel for funding high-risk research that doesn’t fit in the traditional funding channels such as federal grants or wouldn’t be eligible for foundation money. Crowdfunding is similar – it’s basically a type of targeted fundraising that brings in small amounts from many donors, tapping into people who don’t generally think of themselves as philanthropists, but want to see results more tangible and immediate than donating to a large non-profit.

One interesting speaker discussed how they developed small kits, somewhat similar to the chemistry sets I remember playing with as a kid, but focused on biology. They made the point that biotech needs to mind not only their development pipeline, but also the talent pipeline of skilled workers available to do the development. Now, I know what you’re thinking…”we’ve got excess talent in biotech right now. Experienced people are begging for jobs that are beneath them!” If you really think your company is at the point of diminishing returns in hiring smarter people, then why is R&D spending going up every year while the number of new drugs entering the market remains flat?

The three smart people who spoke here are raising money through microfinance and crowdsourcing to bring the ability to do biotech research to schools and interested small groups. What they’re doing is great, but they’ll never be able to have the kind of reach and impact that a company like Invitrogen or Merck could, if they were to start a similar initiative. I’m sure these large biotech and pharma companies are doing some sort of educational outreach, but do they know what these microfinance and open science people are doing and do they realize how effective reaching out to them could be in not only seeding the environment with smart scientists-to-be but simply getting their brand out there in the most favorable light?


Biotechnology, Conferences, Featured, SDBN Blog »

What’s BiotechCamp? A New Way to Share Ideas Is Coming!

Posted by Mary Canady July 11th, 2010 .
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Mary Canady BarcampSD 7 ‘Crowdsourcing Cat Herding’ from Mary Canady on Vimeo.

I presented at a local ‘unconference’ called Barcamp recently in San Diego. The event is great because it is unscripted and interdisciplinary, and we’d like to extend the model to biotech and life science, with the goal of having a ‘BiotechCamp’ in San Diego soon. Check out the presentation, and if you have any ideas, please feel free to add them to the wiki we’ve set up at http://biotechcamp.org. We have a team of about ten now who will be planning this event. As always, tell us what you think and stay tuned!


Drug Discovery, Featured, SDBN Blog »

San Diego Stem Cell Coalition to Fight ALS: CIRM Update

Posted by Mary Canady June 30th, 2010 .
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See photo credits below

Rat hippocampal neurons and astrocytes: See photo credits below

The California Institute for Regenerative Medicine (CIRM) granted a local interdisciplinary research team from UCSD, Salk, and Life Technologies $11.5 million for research aimed at finding a cure for amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease. On June 23rd, CIRM hosted a public research update which I attended. The project is an excellent example of local research organizations and companies working together towards translating research into real cures, funded by California citizens who realize the promise of stem cell technologies.

The ALS team is led by Lawrence Goldstein, Ph.D., and Don Cleveland, Ph.D., from UCSD, and Samuel Pfaff from The Salk Institute. Drs. Goldstein and Cleveland spoke at the event, along with Life Technologies’ Mark Bonyhadi, Ph.D., UCSD’s Martin Marsala, MD, and Lucie Bruijn, Ph.D, from the ALS Association. Goldstein and Cleveland gave a great introduction to the project and explained that ALS is caused by the death of motor neurons, and that the cells’ environment is very important to their survival. Astrocyte cells have a very intimate relationship with motor neurons, and disease progression is predicted to be slowed if healthy precursors are introduced. As Goldstein and Cleveland explained, the ‘neighborhood’ of motor neurons is very important in determining their well being, and healthy astrocytes are the equivalent of neighbors who don’t have parties and mow your lawn for you. The team plans to create and transplant human astrocyte precursors (hAPs) from human embryonic stem cells (hESCs) into human spines. Begining with rodent models, they predict that the first clinical trials could take place in 2014.

Dr. Mark Bonyhadi from Life Technologies then explained how they will help create and analyze the hAPs and develop the processes to prepare them for FDA submission. Life Tech’s long history with high quality cell media and wide-ranging protein and cell analysis tools makes them a perfect partner. Dr. Martin Marsala described the preclinical animal studies that will be performed, and indicated that they have worked with a company called Neuralstem previously to show that spinal cell transplantations can be successful.

Dr. Lucie Bruijn from the ALS Association talked about the fact that there is only one drug available for the disease, and that other stem cell efforts are underway which will help develop the transplantation methods in parallel (Side note: normally drug discovery research is highly secretive, but do publicly funded efforts benefit from removing this veil?). ALS clinical trials are tracked on their website.

The research presented was inspiring, but the clear highlight of the event for me was to hear from ALS patient Dan Desmond. As a veteran, he is unfortunately part of a group that has a higher prevalence to contract the disease, the cause of which is only 10% genetic in nature. From his wheelchair, Dan told us about the progression of the disease, his carpe diem attitude, and he thanked the researchers for their work. Dan received a well-deserved standing ovation at the end of his courageous speech.

Hearing directly from patients is perhaps an unexpected benefit of moving basic research towards a more translational model, where curing disease is viewed as a near-term goal. As described by Dr. Goldstein, CIRM has challenged researchers to rethink assumptions and timelines to come up with solutions to fast-track therapeutics. CIRM is clearly ‘stepping up to the plate’ (pun intended) to make Prop 71′s goals of making California a leader in stem cell therapies come to light. This exciting project pairing our local institutions is a fantastic example of the synergies. Have you thought about who you could work with locally? (Hint: come to our events for ideas…)
Photo by GEHealthcare on Flickr under a Creative Comments License


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Join Us at BarCamp in San Diego July 10/11

Posted by Mary Canady June 18th, 2010 .
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san diego unconference

There’s a cool local event we think would be a great opportunity to explore new ways to communicate science. A group of us are going to BarCamp San Diego, a two day ‘Unconference’ which is described below. Check it out (use link above and more info/register here) and contact us if you’d like to give a presentation, if your company would like to sponsor (very affordable, great for tech-friendly life science companies), or if you’re just interested in learning more.

What is BarCamp?

BarCamp is an international network of “unconferences” where geeks, hackers, makers, and others passionate about Internet culture and technology come together to share ideas and learn from one another. It’s an unconference because there is no theme or pre-set list of speakers – the agenda is built onsite of and by the attendees. Every attendee is expected to be a presenter (but they’re pretty lenient on first timers).

The crowd is largely composed of those from technical fields, but topics can range from handmade books to the biochemistry of beer. All you need is a desire to learn and demonstrate cool stuff to fellow geeks. Admission is free, too! Barcamp is what you make it, so leave the slidedecks at home and get ready to “show and tell”.

Here’s some exemplary pics from previous years:

The SDBN’s eventual plan is to have an unconference completely devoted to life science and biotechnology. To learn more join us at BarcampSD July 10/11!

To share this post easily, cut and paste: Join Us at BarCamp in San Diego July 10/11 http://bit.ly/c12rkD


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The Wonderful World of Wikis for Life Scientists

Posted by Mary Canady June 14th, 2010 .

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