Aarthy › Likes

Hematopoietic hierarchy schemes - scientific masturbation or flow of progress? - Alexey from Bookmarklet

I'll admit I'm somewhat biased given that I worked in an offshoot of Weissman's lab (and I consider him to be the expert of all things HSC-related), but it strikes me that these models present some relatively testable hypotheses: do CMPs exist? do GMPs derive themselves from CMP? do MkEP's differentiate directly from ST-HSC's? - Benjamin Tseng

@ Benj - there are many studies confirmed existence of progenitors (CMP, CLP, MEP...), not only from Weissman group, their relationships and hierarchy is not very clear and under discussion. That's why many labs - mane protocols - many schemes. I have no doubts in Weissman's expertise. He actually accept some alternatives in the canonical scheme, showed for example in his recent review... more... - Alexey

From one of our own - Deepak Singh from Bookmarklet

Also, NAR has a specifically database issue. - Paul J. Davis

"“R is a real demonstration of the power of collaboration, and I don’t think you could construct something like this any other way,” Mr. Ihaka said. “We could have chosen to be commercial, and we would have sold five copies of the software.”" - Ricardo Vidal from Bookmarklet

Well, she's a marketing person, and although SAS is a technology company, they market to executives, not technologists. So I didn't find that rather stupid statement particularly surprising. - Michael R. Bernstein

here is an Ad for a job everyone should want ... - Jim Hardy from Bookmarklet

"We discuss One Laptop Per Child (OLPC) in my senior engineering class on technology and society (STS 401). At the end of the semester, after discussing technologies as being shaped historically by their political, cultural, economic, and environmental contexts, the students do an analysis of OLPC. To Negroponte and the OLPC Foundation, the above issues were all "snags" that came about along the way. They are all, that is, unanticipated consequences. The premise for my students in their analysis was that while the above "snags" might not have been straightforwardly predictable, they were more properly anticipatable consequences." - Bora Zivkovic

Tagged by sennoma under oaos.examples, - Bill Hooker

The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures. - Jim Hardy from Bookmarklet

and Science Now uses the "d-word": decoded. - Neil Saunders from Bookmarklet

@Eva: They may be cute when they are small, but often end up being abandoned when they grow too large. - Eric Jain

Possible, maybe - but limited by the willingness of hospitals to share. - Jere

These guys are all about using aggregating publicly available data sets to achieve better results (or new discoveries) than any one of them alone could. Pretty cool stuff. Disclaimer: they're in my department ;-) - Shirley Wu

nice initial sample size: "Quantitative clinical laboratory data, consisting of 1,104,316 measurements across 656 distinct lab tests. In total, this data represented 4,844 patients across all ages that were diagnosed with one or more of a set of 12 chronic diseases... - Attila Csordas

"A new study shows that the cancer drugs imatinib (also known as Gleevac by Novartis) and sunitinib (Sutent, made by Pfizer) halt diabetes in mice." - Maureen from Bookmarklet

It seems more like prevention to be honest - a stay of execution for the remaining beta cells if the autoimmune problem can be held back, but I'm not sure what it can do once most of the beta cells are destroyed. Of course it might open the way for replenishment (transplantation or recovery of beta cells from precursors)... not sure. Interesting though! (Disclaimer: Just my ideas, not necessarily that of my employer's) :-) - Jo Brodie

Yes, the claim for "halting diabetes" will have to be examined. It'll be good to see the actual PNAS article...this was a press splash before publication. - Maureen

Also, these manyeyes links don't have memory problems (I think...) top 5000 gene pages: http://services.alphaworks.ibm.com/manyeye..., and top 500 gene pages: http://services.alphaworks.ibm.com/manyeye... I'll say it again, Pierre has done some amazing work with this stuff! - Andrew Su

aside from from better labeling of axes, any other comments or suggestions before we finalize things? Any preferences between the java app vs. manyeyes option? - Andrew Su

"Perhaps more importantly, the biotech sector has already adapted to a low-liquidity environment. Financing models for the area were forced to evolve after the technology bubble burst in 2000 and public offerings more or less dried up. Biotech investors and founders are no longer attempting to build the next Amgen or Genentech. Instead, they are building companies to sell, usually hoping big pharmaceutical firms will snap them up. This, says Mott, makes many of today's biotech concerns 'virtual businesses' — they are increasingly outsourcing chemistry and clinical-trials management to places such as India. The deepening economic crisis is likely to accentuate this trend. So it could be good news for Indian scientists who are seeking biotech-related jobs, but it may be less welcome for those in the United States and Europe." - Attila Csordas from Bookmarklet

Not only the virtualization but also they are starting to hire smaller companies to do their basic research, what in the end also reduces costs. - pn

"DNA containing somatic mutations is highly tumor specific and thus, in theory, can provide optimum markers. However, the number of circulating mutant gene fragments is small compared to the number of normal circulating DNA fragments, making it difficult to detect and quantify them with the sensitivity required for meaningful clinical use. In this study, we applied a highly sensitive approach to quantify circulating tumor DNA (ctDNA) in 162 plasma samples from 18 subjects undergoing multimodality therapy for colorectal cancer. We found that ctDNA measurements could be used to reliably monitor tumor dynamics in subjects with cancer who were undergoing surgery or chemotherapy. We suggest that this personalized genetic approach could be generally applied to individuals with other types of cancer." - Attila Csordas from Bookmarklet

I love the Umbrella Corporation soundtrack on the video, too. :-) - tim from Alert Thingy

Been hunting locally for students but so far no takers. This project would follow on the Gene Wiki effort, specifically by creating a poster-sized visualization for the growth of the Gene Wiki over time. The project involves using the MediaWiki API, database inserting and querying, and SVG output. Some minimum programming skills are required, but all the specifics could be learned "on the job". I'd estimate 2-4 months work at half-time. Questions/inquiries welcome here or at asu@gnf.org. - Andrew Su

Pierre++ - Deepak Singh

Applied Biosystems Primer Express, mainly because we use a lot of MGB probes. - Nils Reinton from twhirl

Stratagene's design tools + Vector NTI - Aarthy

"Free poster and podcast (Nature Genetics/Nature Reviews Genetics)" - Maxine

Only too true... - Björn Brembs

FWIW, I have mentioned this idea to a guy from the NSF I know and he vowed to establish a grant lottery. - Björn Brembs

"Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects." - Attila Csordas from Bookmarklet

"An integrated cell-free metabolic platform for protein production and synthetic biology Michael C Jewett1,a, Kara A Calhoun1, Alexei Voloshin1, Jessica J Wuu1 & James R Swartz1,2 Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA Department of Bioengineering, Stanford University, Stanford, CA 94305-5444, USA" - Maxine from Bookmarklet

"......central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe... more... - Maxine

In in SF attending Collaborative Drug discovery Meeting, learning about special software now. Will keep you posted. - Maureen from Bookmarklet

I've been curious as well. I like the concept, but there are so many other challenges here - Deepak Singh

Bora I'm using PLoS ONE as an example of Science in Web2.0 for my cheminfo class tonight http://friendfeed.com/rooms... - Jean-Claude Bradley

Lovely! Thank you. - Bora Zivkovic

"Sharing biomedical research and health care data is important but difficult. Recognizing this, many initiatives facilitate, fund, request, or require researchers to share their data. These initiatives address the technical aspects of data sharing, but rarely focus on incentives for key stakeholders. Academic health centers (AHCs) have a critical role in enabling, encouraging, and rewarding data sharing. The leaders of medical schools and academic-affiliated hospitals can play a unique role in supporting this transformation of the research enterprise. We propose that AHCs can and should lead the transition towards a culture of biomedical data sharing". - Graham Steel

"Whenever a new member joins the site, they are asked to identify themselves by both their department (for example, Computer Science), and then a more narrow field (example: Search Engine Algorithms). From then on, all activity submitted by this user will be added to the feeds of the fields they participate in. The site also allows users to specify certain members using a Twitter-like “Follow” system. Academia’s success will lie in its ability to build a useful news feed revolving around its professional network" - Attila Csordas from Bookmarklet

And to the question about A&I services, so far as I am aware these services simply reproduce the abstract, title and author list of the paper itself, which the journal supplies. - Maxine

Who could that be :)? - Deepak Singh

LOL - Aarthy

I am putting together an informal presentation summarizing Tufte's ideas. The audience is a room of software engineers and computational biologists. I always enjoy hearing people's interpretation of Tufte's work. - Sutee Dee

My own MO in graphics is to apply Tufte's aesthetics to Cleveland's ideas of data presentation. - Chris Cotsapas