The Life Scientists

"For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop" - Bill Hooker from Bookmarklet

From Johnathan Eisen's twitter: http://twitter.com/phyloge... - Steve Koch from Bookmarklet

Try: http://twitter.com/phyloge... - Jim Till

Thanks, corrected - Steve Koch

"We have generated and made publicly available two very large networks of molecular interactions: 49,493 mouse-specific and 52,518 human-specific interactions. These networks were generated through automated analysis of 368,331 full-text research articles and 8,039,972 article abstracts from the PubMed database, using the GeneWays system." - Attila Csordas from Bookmarklet

authors are not humble: "We described and made publicly available the largest existing set of text-mined statements; we also presented its application to an important biological problem" - Attila Csordas

Oh no, that's terrible news... how did you hear?? - Shirley Wu

Please drop your comments here http://warrendelano.blogspot.com/2009... - Abhishek Tiwari

"[This study is] the successful first clinical testing of an HIV-derived vector in hematopoietic stem cell (HSC)–based gene therapy. The procedure was used to treat a severe neurodegenerative disease, X-linked adrenoleukodystrophy (ALD), and the results indicate stable expression of a therapeutic gene in a substantial fraction of patients’ hematopoietic cells, as well as clinical benefits." - Ruchira S. Datta

who's asking you to do this? the editors? as for what it means: http://en.wikipedia.org/wiki... – but that wouldn't be a positive thing to put in a paper. I don't know what your findings are, but perhaps you can argue "you only find what your method of detection could possibly find" like in the different methods of looking for protein complexes http://www.sciencemag.org/cgi... - Michael Kuhn

That would be ok if there were other "mechanisms to cause X", but here "X" is the presence of this bacteria. Our method is not in dispute, nor is the quality of that method, presumably then, it's agreed upon that our method explains 100% of the cases, and I still do not understand what the editors want from us. I would if this was a question of the specificity or sensitivity of the method, but even then the statement would make little sense to me. - Nils Reinton

"Yesterday I attended a biweekly meeting of an informal UC Berkeley group devoted to Python in science (Py4Science), organized by Fernando Perez. The format (in honor of my visit) was a series of 4-minute lightning talks about various projects using Python in the scientific world (at Berkeley and elsewhere) followed by an hour long Q&A session. I was blown away by the wide variety of Python use for scientific work. It looks like Python (with extensions like numpy) is becoming a standard tool for many sciences that need to process large amounts of data, from neuroimaging to astronomy... [see list of very interesting TOPICS and projects]." \\ see also http://fperez.org/py4scie... which includes links \ Video at http://www.archive.org/details... - Adriano from Bookmarklet

more details on where the big $12.2-million grant goes to:"The site's algorithm searches for scientific topics, and VIVO yields detailed 'hits' broken down into the most relevant subcategories — such as researchers, activities, events, organizations, publications or subtopics related to the term. "If you search for people, you'll just get people," says Conlon" - Attila Csordas from Bookmarklet

"We are increasingly keeping scientific records in electronic form; it would be straightforward to wrap our notebook pages describing an orphan result with a bit of searchable text, generate a web page, and submit the whole thing to a database. The act of conducting research would thus become practically synonymous with the act of disseminating the resulting knowledge. Along the way, we would have to spend some energy improving the records that we keep in order to ensure that our notebooks were more accessible to outside readers and less like the quirky private diaries they often become." Heh. - Heather

.. and if this could result in a proper citable reference on the other end, that'd sweeten the deal :) See e.g. Jean-Claude Bradleys comment near the top of this thread, about 'dumping' data to Nature Preceding to get a reference + DOI in return: http://friendfeed.com/the-lif... - 'Mummi' Thorisson

I'd really like to see that refactored as a collaborative Google Wave gadget. - Dan Hagon

@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years... - Martijn van Iersel

Great piece! I especially like the delineation of types of "negative" results - results that aren't even "negative", but just were deemed unpublishable for some reason or another. It does seem that a lot of the practical barriers would be overcome by self-publishing online through electronic notebooks or blogs, with minimal effort, but minimal is still some... - Shirley Wu from twhirl

Great post about data standards from someone who's been working with them from ODBC to AJAX to XML, with a focus on healthcare data standards but relevant to life science, particularly point 2. - Mr. Gunn from Bookmarklet

"One problem that I am facing is convincing colleagues of the utility of an Open Access publication. ... Not everyone operates on large grants. Many lab budgets leave very little room to buy a new laptop, let alone pay for an OA publication (typically the price of two of said laptops)." - Mickey Kosloff from Bookmarklet

Good points here. Proving a rival to current closed-access or setting a precedent to get grant-givers to make line-items for OA publication are good in an abstract/aggregate level, but the individual lab decision-maker is thinking on a lot more concrete terms. Perhaps, some sort of Impact Factor or "open access journal news" to add credence/credibility can substitute? - Benjamin Tseng

I'm glad you've made the point -- I talk about it with students who will have to make these kinds of decisions in the coming years -- and it's a tough one: ideological belief against practical action. Maybe we need a kind of OA investment account where interest can be accrued over the life of a grant. Okay, not realistic...government subsidies, maybe;-)? - Mickey Schafer

The Research 2.0 Concept Model above is an evolution of the Academic Library 2.0 Concept Models developed for my Master's Paper (http://mchabib.com/2006... ). While the original model primarily focused on academic library services for students, the new model focuses on services for researchers. Like in the original models, the top represents communication spaces grounded in physical space, while the bottom mirrors this in the online realm. Two ends of the spectrum are informal communications and formal communications. My argument is that Research 2.0 falls somewhere between these extremes. A full presentation is located here: http://www.slideshare.net/habibmi... - Michael Habib

Interesting social status implications here, especially with the second model. The more robust both sides of the scholar2.0 identity components (UGC + trad), the "deeper" the 2.0 identity (think tag clouds as the metaphor here). Or, perhaps color combos is a better metaphor, with schol.identity2.0 being a mix of UCG (say, "yellow"), trad (say "blue") and combo being "green" -- the shade... more... - Mickey Schafer

"We give a "hoot" about our students' education! My school cares about engaging students and providing them opportunities to learn. We are in a high-need, urban community which strives to meet the needs of all students. Currently, I teach third grade students from a variety of different backgrounds and academic abilities. The student population is highly transient and requires additional support from teachers and educators to provide experiences to help them be successful in school. Students are fascinated by birds of prey, especially owls, and are eager to learn more about them. I want to develop a theme unit that expands the knowledge of third grade students, but I lack the resources to do this. We have minimal supplies in our library and science lab to support student interest. All third grade students will have an opportunity to learn about birds of prey. Our teachers will develop a unit of study which focuses on the owl. It will integrate science and language arts. We need 14... more... - Mike Chelen from Bookmarklet

I donated $25.00 -- think I will do this site from now on instead of Christmas presents with some of my adult friends -- my brother and I have begun donating to charity instead, and I like the way this site lets one choose specifically. - Mickey Schafer

FYI: donors received thank-you note from teacher this morning b/c project met funding goals. Cool! Also can find on site the subsequent activity including ordering and mail receipt of materials. This is a really neat site. Will look for a button to add to univ. web page. - Mickey Schafer