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Anil Thomas › Likes

Abhishek Tiwari
"This paper presents an alternative visual web-enabled interpretation of the short-based graphical sequential narration titled Nature vs. Science, pt. 1 (NAT). It is hypothesized that use of this secondary interface suffused with third-person linguistic usage and academic spatial distribution will provide improvement in perceived acumen generated from stochastic interactions with supervisory archtypes found in learning environments. Results show that persistent exposure to phdcomics dot com (PDC) is mildly correlated to jocular deportment, which suggests improvements in temporal-delay behavior of bounded activity. " - Abhishek Tiwari from Bookmarklet
I have now learned that the unit of impact factor is "inches" :-D - Nils Reinton
"If only you had that problem" LOL - Yann Abraham
Abhishek Tiwari
Great acts are made up of small deeds: NextBio, Microfinancing and Microfunding in science: This is not a secret.. http://www.abhishek-tiwari.com/2009...
Congrats :-) - Madhu Pandey
Rajarshi Guha
Deepak Singh
Arvind Narayanan's journal - Bioinformatics needs to be democratized - http://arvindn.livejournal.com/109389...
If it were only this easy. That said, there is a lot of data available. Have away my friend - Deepak Singh from Bookmarklet
you said it :) - Deepak Singh from IM
I don't think its a versus post, more of a "we're lacking this core group of programmers, which is a shame cause we could use a *lot* of them" type of post. I tend to agree in that its a shame that bioinformatics isn't driving more innovation in software than it is, although, I'm not convinced that docs are the largest hurdle to navigate in recruiting hackers. - Paul J. Davis
Deepak Singh
Abhishek Tiwari
Haskell for Bioinformatics: Ketil Malde has developed a functional-flavored bioinformatics library in Haskell fo.. http://www.abhishek-tiwari.com/2009...
Abhishek Tiwari
Another Blogger Leaves the SEED Blogs (ScienceBlogs.con) - http://sandwalk.blogspot.com/2009...
Abhishek Tiwari
How impact factor game is hampering translational research - http://www.abhishek-tiwari.com/2009...
How impact factor game is hampering translational research
Abhishek Tiwari
Big Data: Hadoop is tuned for availability not efficiency: A very interesting post by UC Berkeley Professor Joe .. http://www.abhishek-tiwari.com/2009...
SDD will hopefully make the checkpointing work efficiently for the optimists and pessimists. - Todd Hoff
Abhishek Tiwari
U-Compare: Advanced Biological Text Analytics Using Workflows - http://www.abhishek-tiwari.com/2009...
U-Compare: Advanced Biological Text Analytics Using Workflows
Play
novoseek
Is the swine flu "infecting" social medias? We try to give an opinion on KBW. Worth read it http://blog.novoseek.com/index...
Abhishek Tiwari
Model validation is actually a misnomer - http://www.abhishek-tiwari.com/2009...
Lot of heat out there in comment section :-) - Anil Thomas
Deepak Singh
confirmed. Giving a talk at Janelia Farms on Monday. @hyphaltip thanks
Nice, do report back if any interesting synergy turns up from meeting with folks there. I am thinking more about how I might invest in using EC2 in my new lab to augment a smaller (local) cluster purchase. - Jason Stajich
Abhishek Tiwari
MapReduce is now reaching mainstream science - http://www.abhishek-tiwari.com/2009...
There's also the work by DE Shaw which I wrote about last year http://mndoci.com/blog... - Deepak Singh
@Deepak thanks for that link, that seems an interesting real time application - Abhishek Tiwari
Abhishek Tiwari
"how Hadoop is being used to process the results from High-Energy Physics experiments" - Abhishek Tiwari from Bookmarklet
Abhishek Tiwari
Open Standards: Restructuring, Modularization and Resizing - http://www.abhishek-tiwari.com/2009...
Abhishek Tiwari
"Technology luminaries pick the chips that changed the world— and their lives" - Abhishek Tiwari from Bookmarklet
Gordon Moore, Vinod Khosla, Jeff Hawkins and many others pick their favorite chips, featuring a whole generation of processors - Abhishek Tiwari
Abhishek Tiwari
A biosystem, or biological system, is a group of molecules that interact in a biological system. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs. - Abhishek Tiwari from Bookmarklet
Deepak Singh
Computational Thinking - http://mndoci.com/blog...
It often is hand wavy, especially since many of the advocates make it more complex than it needs to be. It's one reason I admire Jon so much. I actually grasp complex subjects when filtered by him - Deepak Singh
Jeanette Wing's article was very nice as well, http://tinyurl.com/dyrkjv. Her examples are nice, especially for people with no to little background in computing (making dinner on sunday night and eating for the next few days is caching :) - Rajarshi Guha
Check out the new podcast as well. That's the second one in the series and really got me thinking. http://bit.ly/ByZKS - Deepak Singh
Abhishek Tiwari
Abhishek Tiwari
genereg
I have a question about predicting transcription factor binding sites. For human, the UCSC Genome Browser does this using the Transfac weight matrices. But I can not find such a feature for Drosophila. Any suggestions? Thanks
I have used REDFly [ http://redfly.ccr.buffalo.edu/... ] and FlyTF [ http://www.mrc-lmb.cam.ac.uk/genomes... ] to get TFBS info for some DMel genes. I am not sure if these resources are integrated with UCSC Genome Browser. - Khader Shameer
Thanks for the link. However they only give experimentally known binding sites and don't do computational prediction of TFBS... Are there any other resources? - genereg
May be you can try NNPP [ http://www.fruitfly.org/seq_too... ] ? I am not sure about whether the data set used for training contains the TFBS data that you are looking for - better to check the TFBS data before you try this. - Khader Shameer
Interesting link, thanks. No computational prediction tools, but still a very nice link. - genereg
So, does anyone know whether a database like Transfac exists for Drosophila transcription factor weight matrices? - genereg
Thank you, Carl - genereg
This page http://rana.lbl.gov/eisen... includes a program called TFEM "Transcription Factor Expectation Maximization, an algorithm for detecting DNA regulatory motifs by incorperating positional trends in information content." I don't know anything about it, but I would think they must have used it for Drosophila. If you're interested I could go down the hall and ask some time... - Ruchira S. Datta
Björn Brembs
In which Calvin & Hobbes manage to capture creationism - http://bjoern.brembs.net/news...
seriously though, making evolution and neuroscience understandable and non-threatening to non-scientists is a big f***ing challenge - Christopher Harris
Maybe some belief systems ought to be threatened? :-) - Björn Brembs
that kind of dismissive attitude leads to what happened in germany just now http://scienceblogs.com/genetic... people are afraid - Christopher Harris
Many Germans today are scared of the future and believe the best solution is to go back to the stone age. I seriously doubt that challenging religious viewpoints with science is even close to the top reasons for that attitude. Germans simply don't care enough about religion - especially now after the recent pope incidents. Moreover, in principle, from a politician's perspective, it may sometimes be prudent to prevent access to a technology and then allow access after public pressure. Gun laws spring to mind - Björn Brembs
That's a interesting observation, Björn. The fear of new ideas often has little to do with the ideas that are being replaced, and possibly more to do with lack of understanding of the new idea rather than resistance to it for orthodox reasons. Sounds to me like the only way around that is educate people earlier and better. - Mr. Gunn
it's not just about education and I don't think there's anyone in particular to blame (except maybe michael crichton..) - people are concerned about where this whole science thing is going, who's in charge? and not being personally familiar with evolution and these little nucleotides that have replaced the warm and unfathomable mother nature (or god) of their childhood, they respond... more... - Christopher Harris
I said it's not _just_ about education and explaining how things work: there's an existential dimension that I think scientists are prone to ignoring - Christopher Harris
Deepak Singh
Abhishek Tiwari
Abhishek Tiwari
A Sneak Preview of Wolfram|Alpha: Computational Knowledge Engine | Berkman Center - http://cyber.law.harvard.edu/events...
This event will be webcast live at 3:00 pm ET on 4/28 from this link: https://cyber.law.harvard.edu/interac.... - Abhishek Tiwari from Bookmarklet
Abhishek Tiwari
novoseek
"Access Points in novoseek". Find in this detailed information page how Access Points work in novoseek. Thanks to this, you should be able to explore more of the content and create very specific requests. We are very interested in having your feedback on it. Thank you - http://novoseek.com/AccessP...
For instance, if you want to earch for the gene "alpha synuclein" using the GenBank ID CR457058. The link structure should be this one http://www.novoseek.com/AccessP... - novoseek
Björn Brembs
There is but one journal: the scientific literature - http://www.plosmedicine.org/annotat...
"This is where the basic distortion of science occurs: when an individual scientist with a new idea has to expose it to the scrutiny of "intermediary" peers before having the money to test it and believe it or not themselves. The simple cure for this is no-questions-asked baseline funding, perhaps proportional to average salary, recognizing that society has already made a huge investment of trust and money in scientists via their education, hiring, promotion and tenure[2]." - Björn Brembs from Bookmarklet
Professor Gordon posted his comment on my blog: http://bjoern.brembs.net/comment... - Björn Brembs
Wow, I missed the discussion on the baseline grants: Gordon, R. & B.J. Poulin (2009). Cost of the NSERC science grant peer review system exceeds the cost of giving every qualified researcher a baseline grant. Accountability in Research: Policies and Quality Assurance 16(1), 1-28. - The Neurocritic
ooops, I haven't even noticed, until now, that Dick Gordon is one of the authors of the NSERC paper... and he commented on my blog. I feel so honored now! - Björn Brembs
A possible follow-up to the NSERC study is being discussed at http://friendfeed.com/e... . Please take a look and comment. - Daniel Mietchen
"Science is subject to great uncertainty: we cannot be confident now which efforts will ultimately yield worthwhile achievements. However, the current system abdicates to a small number of intermediates an authoritative prescience to anticipate a highly unpredictable future" Very good stuff! - Kevin Gamble
Also check the discussion here: http://friendfeed.com/e... and here: http://scienceblogs.com/clock... - Bora Zivkovic
Got the author on to friendfeed: http://friendfeed.com/dickgor... - Björn Brembs
Iddo Friedberg
Holy Cow! Bovine Genome and Bovine HapMap papers published - http://www.sciencemag.org/cgi...
"The bovine HapMap data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation," University of Missouri researcher Jerry Taylor, who was part of the Bovine HapMap team, said in a statement. "The recent decline in diversity is sufficiently rapid that loss of diversity should be of concern to animal breeders." - Iddo Friedberg from Bookmarklet
Overall, indicine cattle, humped cattle found in South Asia and East Africa, had higher SNP diversity than taurine cattle, humpless cattle found in Europe, Africa, Asia, and elsewhere. For instance, Brahman cattle had a SNP every 285 base pairs — the highest level of genetic diversity observed in cattle breeds so far. Holstein and Angus breeds had about half as many SNPs. - Iddo Friedberg
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