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The Life Scientists

The Life Scientists

A room for all the life science types on FriendFeed (and everyone we've co-opted). Topics tend to focus on bioinformatics and computational biology, but discussion from any area in biological sciences is welcome. Try not to spam and if you are associated with a service (and most don't know that), please say so.
Blog
Carl Boettiger
What advice would you give to new graduate students about creating a webpage & establishing a web presence?
For the web page, you could create a page on github like Egon did: http://egonw.github.com . Establishing a web presence: blog your research and comment the other blog, Q&A sites etc... - Pierre Lindenbaum
I would suggest starting your own site. Github is a great option if you're a coder. Get on Biostar and similar sites. - Deepak Singh
So most labs have a lab website to which a student can add their own webpage. This gives the advantage of discovery from those coming to the lab page, and both the discovery advantage and the 'professional' look of a university url, but some of that becomes a disadvantage when the student moves on. Should new graduate students be buying a lifetime url for themselves? - Carl Boettiger
IMO anyyone interested in a professional career should. Good examples in addition to Egon's are Bosco Ho (http://boscoh.com/) and Neil/Pierre's blogs which highlight the things they are interested in. - Deepak Singh
My advice would be to buy your own domain and get a cheap webhost. You will be moving around often enough before you get a permanent job that putting your stuff into a university system is counterproductive, especially if they have a proprietary CMS. Put Wordpress on your domain because it is easy enough to use and can be used as a CMS and/or a blogging platform. Make sure that finding... more... - Matt Leifer
Agree with Matt and Deepak -- potential employers search using google. It is important that either the individual has crafted what people can find OR the individual isn't there at all. Not sure what will happen as long-term use emerges, and folks find pasts they wish not so obvious present when building a professional portfolio. - Mickey Schafer
The first advice should probably be to change their name to disassociate themselves from the drunk Facebook pictures and to pick a unique enough name... - Eric Jain
I'd say "just do it". It's easier than ever, but one issue is the large number of choices. I'd suggest starting out with a hosted service (e.g. Wordpress.com) - you can always switch to self-hosting later, if you feel the need and are prepared to put in the extra work. There are plenty of good, free wiki/blog services. I think the basic choices are between simple "about me" web page,... more... - Neil Saunders
I started my website as a graduate student in the mid-90s on a university server. Towards the end of my PhD, 1999 I got my own domain, as it was clear I'd be moving institutes for the forthcoming years. Started a blog in 2003. I think today, a student only needs a blog, as any more permanent information can be linked as separate pages from that blog. - Björn Brembs
I had this discussion with students on the ESOF conference a while ago, here my recommendations I gave them ... Scientific presence - Never forget that it is about you - http://bit.ly/dqu84l #science #web #presence - - joergkurtwegner
@Carl - Lab pages are certainly a good temporary solution, and they do typically not ensure long-term stability. So, I would recommend another solution, and nowadays no one has to pay for a good long-term web presence. @Eric - Agreed - Name consistency and trust building are important, it is simple, people will find you anyway, so do not try masking anything, it will not work. Be honest! - joergkurtwegner
get your own site, most lab sites are unstable and really annoying to update. I think you have basically two options - make an online CV on steroids (link to papers/code/data/etc) or start a blog. however, starting a blog is trickier than it sounds. an abandoned half-assed blog is worse than no blog at all. honestly, it takes at least a few months before you find your voice. that said,... more... - Bosco Ho
I usually suggest to my students that create a FriendFeed account and start interacting with people in their field of interest. Later they can decide if it makes sense to start a blog, wiki, etc. - Jean-Claude Bradley
Isn't friendfeed too small? Twitter will have a much larger group in any discipline, though in 2010 blogging is not arcane so anyone can set up something good if they want to maintain it; it's just finding a theme you like and not expecting a million readers a month without some effort. - Science 2.0
Mateusz Koryciński
Nanobiotechnology Advances Point to Medical Applications - http://www.sciencedaily.com/release...
Ami Iida
Model for Implantable Artificial Kidney to Replace Dialysis Unveiledhttp://www.sciencedaily.com/release...
kidney100902161253.jpg
Andrew Su
Who gave the best talk in systems biology (broadly defined) that you've seen in the past year?
Iddo Friedberg
The open source spammer: extracting email addresses from an openoffice.org document #Linux #OSS - http://bytesizebio.net/index...
Duncan Hull
What happens when you teach monkeys to use money? « O'Really? - http://duncan.hull.name/2010...
What happens when you teach monkeys to use money? « O'Really?
Freakonomics and its successor Superfreakonomics are two books by the economist Steven Levitt and his partner in crime Stephen Dubner that have a common theme running through them (quote): “People respond to incentives, although not necessarily in ways that are predictable and manifest. Therefore, one of the most powerful laws in the universe is the law of unintended consequences.” Both books give numerous and often amusing examples of the ways that various incentives often result in unexpected outcomes. They choose a wide variety of animals including teachers, sumo wrestlers, estate agents, bible salesmen and yes, monkeys, to illustrate this point... - Duncan Hull from Bookmarklet
Manuel
myKaryoView: First Open Source Visualization Software for 23andMe Data http://networkedblogs.com/7qu5l
Ruchira S. Datta
Reminder: I'm liveblogging the Human Microbiome conference at http://friendfeed.com/human-m...
You're the toughest liveblogger I've ever seen. :) Keep up the good work. - Attila Csordas
Duncan Hull
How Many Unique Papers Are There In Mendeley? « O'Really? - http://duncan.hull.name/2010...
How Many Unique Papers Are There In Mendeley? « O'Really?
"Mendeley is a handy piece of desktop and web software for managing and sharing research papers [1]. This popular tool has been getting a lot of attention lately, and with some impressive statistics it’s not difficult why. At the time of writing Mendeley claims to have over 35 million papers, added by just under half a million users working at more than 10,000 research institutions around the world. That’s impressive considering the startup company behind it have only been going for a few years. The major established commercial players in the field of bibliographic databases (WoK and Scopus) currently have around 40 million documents, so if Mendeley continues to grow at this rate, they’ll be more popular than Jesus (and Elsevier and Thomson) before you can say “bibliography”. But to get a real handle on how big Mendeley is we need to know how many of those 35 million documents are unique because if there are lots of duplicated documents then it will affect the overall head count...." - Duncan Hull from Bookmarklet
I'd like to see a distribution of those ~ "36 000 000" papers across the 487 953 users; I wonder how much of a long tail there is (users with very few papers). - Neil Saunders
@Neil me too, I bet it follows a classic long tail distribution, with a core of very active users and lots of inactive ones with one or two papers - Duncan Hull
That's what I'd expect, as well. I left a much longer comment on the blog post, but essentially, the numbers are as correct as they can be right now, and should be reasonably accurate as they are. Better stats are coming, but really, the story here is that Mendeley has crowdsourced what will soon be the world's largest database of research, and we're letting anyone, man or machine, query it for free. - Mr. Gunn
I know that sounds like I'm just tooting Mendeley's horn, but come on... People don't fight (that much) with Facebook about whether they have 450 million or 500 million users, because it really doesn't matter, does it? They're still the largest by an order of magnitude, right? - Mr. Gunn
Mr. Gunn, when you quote user numbers, what are you counting? Is it registrations, some definition of activity or something else? - Kevin Emamy
@Mr Gunn thanks for the comments. I don't think the data (IMHO) supports the claim of "what will soon be the world's largest database of research" (36 million documents), I left some details in a comment on the original blog post. - Duncan Hull
The "claim" made on the Mendeley homepage is that there are 36M+ docs currently in user libraries. Meaning that users have added 36M docs. That is as true as true can be and really isn't hard to understand when you look at the progression as a function of time since we launched in January 2009. We have repeatedly said in talks and in writing that this is not a unique count and that... more... - Jason Hoyt
Just to be clear, the fake initials comment is re: a commenter on Duncan's post, not anyone on friendfeed. - Mr. Gunn
Kevin - the user numbers are active accounts, but I don't presently know exactly how that is defined. It's some measure related to account age, number of documents in the library, date of last upload, profile completeness, etc. - Mr. Gunn
@Jason interesting stats, didn't know that there were that many academic documents. It's probably just me being pedantic but I think the claim at http://www.mendeley.com of "36,203,549 Documents in people's libraries" is potentially misleading (especially when compared to WoK and Scopus) because it doesn't explicitly specify if this is de-duplicated or not. The Scopus and WoK figures of... more... - Duncan Hull
It is really exciting to see a free and weighted reference/citation network being created. I certainly hope that mendeley continues to grow. Still, I agree with Duncan that it would be informative if mendeley could find ways to collapse those documents and authors. I realize this is a hard problem. - Pedro Beltrao
@Pedro yup, I hope Mendeley will continue to grow too (and get better stats along the way) - Duncan Hull
Pawel Szczesny
Help needed. I have a manuscript on analysis a family of (mostly) bacterial toxins, that due to various circumstances had been rewritten dozen times over the last three years. It's basically complete, but I lost any sense of its correctness. Anybody willing to do a rough proofreading (really rough) and comment on research?
Due to multiple authorship (from different institutions), I cannot post the manuscript here - if anybody is willing to help, I will send the manuscript via email. - Pawel Szczesny
I'd be happy to. You have my GMail address? - Neil Saunders
If you want, send to me too. When do you need it back? - pn
Neil, sure I have. Paulo, I don't know - next week? It's hopefully not very time consuming. Thank you both - will send the manuscript in a moment. - Pawel Szczesny
Mateusz Koryciński
New system using bacterial communities to solve complex problems - http://www.sciencedaily.com/release...
Mateusz Koryciński
Jim Hardy
34 new stem cell journals since 2004: is this a good thing? - http://arstechnica.com/science...
34 new stem cell journals since 2004: is this a good thing?
I'm curious how many are Open Access? - Jim Hardy from Bookmarklet
me too: eeeh, this article is in a non-OA journal so I cannot see the list ;-) - Claudia Koltzenburg
I've count 3 OA stem cell field-related journals, appeared after 2004: (1) http://stemcellres.com/ (2) http://www.sage-hindawi.com/journal... (3) http://www.ctt-journal.com/ - Alexey
We need to stem the flow... - Noel O'Boyle
how would you suggest doing this as authors, @Noel O'Boyle? - Claudia Koltzenburg
(Sorry Claudia, it was just a lame pun.) - Noel O'Boyle
+2 more: (4) http://www.dovepress.com/stem-ce... (5) http://www.ingentaconnect.com/content... Former is the new branch of Cell Transplantation, which exist many years. - Alexey
Iddo Friedberg
Iddo Friedberg
Science, Reason and Critical Thinking: Modern Science Map - http://crispian-jago.blogspot.com/2010...
Science, Reason and Critical Thinking: Modern Science Map
Mateusz Koryciński
Scientists unveil structure of adenovirus, the largest high-resolution complex ever found: http://www.eurekalert.org/pub_rel...
Pretty. "The pair also made the realization that they had the most success with fresh crystals that had just completed their two-month growth cycle. The scientists started timing their trips to Chicago to coincide with the period when the crystals were freshest. Nemerow and Reddy began travelling to Chicago at least three times a year, grateful that their hosts in Chicago were willing... more... - Matthew Todd
Antony Williams
For those of you who have watched the ACS versus Leadscope case, the Leadscope response to the ACS appeal to the Ohio Supreme Court was filed today http://www.sconet.state.oh.us/tempx...
Ruchira S. Datta
Björn Brembs
Online commentary on papers allows scooped authors to argue their priority? | DrugMonkey - http://scientopia.org/blogs...
Very quickly read this - but couldn't the publication decision have been based on whether the paper was well-written or not? i.e. less about the data, and more about whether the paper was good? - Matthew Todd
@Matthew, but should that be a consideration for seeing a paper through? When I review I look at the data for a decision of letting a paper through and then work on the writing. But if the data is solid, wrtiting flaws should not per se (in my opinion) be a reason for rejection. - Kubke
Oh I agree, but we're humans and you can't blame a referee for being so bored/irritated that they fail to engage with the paper. Helping readers engage is why we have abstracts, introductions and conclusions. They add no new data. - Matthew Todd
Some more nuance in the comments. Either way, I'd like to hear the explanation of the editor, who, according to the comments, was a former lab-member of one of the authors of the accepted paper. - Björn Brembs
Carl Boettiger
I'm looking for a good solution to upload figures into my open lab notebook. Need fast, many photo, automated / scriptable uploading, permanent hosting, with searching/tags/comments. Trying photobucket: http://openwetware.org/wiki... Thoughts?
I think ideally I would run a script which would run some code which generates a png figure, pushes the photo to the host site under a given album/tags and a link to the version of the code that created the figure on the project's github site. Since the codes take a long time to run, simply having the code version is no longer sufficient for me. - Carl Boettiger
Have you considered the possibility of using Flickr to host the photos? They have an API, are quite inexpensive and I know that there is/was a plugin to add Flickr images easily into OWW (mediawiki). - Ricardo Vidal
Yup, Flickr seems very promising since there's lots of development around it. Do I need to buy a subscription to make sure the uploads are permanent? Think I'll give it a try... - Carl Boettiger
No, all uploads are permanent and I believe you can "display" up to 200 images for free. The last 200 are always visible and nothing is lost. If you pay the $24 USD/year, all images become public/visible again. - Ricardo Vidal
Flickr seems to be a nice solution. With one command-line call I can have a full slideshow of results embedded into the notebook! http://openwetware.org/wiki... Each image can collect comments and other tags and be organized into groups. the command-line upload also doesn't seem to spam my FF/twitter feed even though I added flickr to FF. guess that's a good thing. - Carl Boettiger
Vedran Rodic
Five scientists discuss their hopes and aspirations for biotechnology in a post-genomics era. - Vedran Rodic from Bookmarklet
Great episode. Got somewhat irritated by Marc's IP comment on the beginning, but great episode either way. - Vedran Rodic
Iddo Friedberg
Benjamin Good
Anyone have an idea how to quantify this statement "Currently, a large part of this biological information (such as the function of a protein) is presented in the scientific literature, but is not captured in any database" ?
Nope - I've only ever seen handwaving estimates. Would love to see some figures with at least solid reasoning behind them. - Cameron Neylon
Me too.. I wonder if there is some information-content metric that could be applied to text and compared to databases. - Benjamin Good
Well, if you go to the library, and measure the shelf space given over to journals, it will be many many metres, while swissprot takes no space at all. - Phil Lord
What we're really talking about here is the degree to which something is marked up or machine readable vs. formatted for human consumption, right? - Mr. Gunn
Kind of. If you view the scientific literature as a collection of facts represented in text that could be represented in databases, how many of the facts are still sitting in the text? - Benjamin Good
I wonder if you could run a selection of papers through http://sourceforge.net/project... and see what percentage of just the table are able to be extracted? - Mr. Gunn
Lars (http://friendfeed.com/larsjuh...) has been doing large scale text mining ... he might be in a good position to give you some sort of a guess on this though I am not sure how would you quantify this. - Pedro Beltrao
Fact mining tools like tableseer (thanks mrgunn, that is cool) and textminers (e.g. http://code.google.com/p...) seem like a reasonable place to start. Precision is always a problem with these, but if we dialed the recall all the way up, perhaps we could approach an estimate on an upper bound. One difficulty is the lack of available full text - but we could make some guesses.. - Benjamin Good
maybe another way to think about this is to look at some of curation efforts that have been done to date to see how much (on average) was extracted from those papers that were curated and extrapolate to all other papers. - Pedro Beltrao
one related, squishy data point I can provide is that, for the ZFIN database, only about 10-20% of the papers that are curated result in any GO annotations at all. We could use this, plus the number of annotations extracted per article to estimate the number of annotations missed in uncurated articles. - Benjamin Good
the STRING database aggregates information from experiments, databases and text-mining. So you could download the detailed protein links from http://string.embl.de/newstri... and compare how many interactions you get from the different evidence types. Caveat: text-mining is largely based on co-occurrence. - Michael Kuhn
I guess a crude measure would be to count the occurrences of a protein symbols within a paper. You could download the PMC OAI set and use this as a model for the entire PubMed dataset. - Mark Fortner
Does a blob of unstructured text in a database count as "captured" information? - Eric Jain
To Eric I would say no. To Michael and Mark, I think STRING is hitting closer to the mark. - Benjamin Good
Same statement (but still no quantification) in Cheung et al., from Gerstein Lab: "[...] there is a large bulk of unstructured data that is deeply buried in the literature (e.g. journal papers) and as a result, is not readily accessible for inclusion in additional analyses". Just published on MSB: http://bit.ly/9atIIq - Salvatore Loguercio
Exactly.. You see this everywhere (including in things that I have written) but it seems that no one ever can/bothers-to/attempts-to put a bound on the problem. Maybe its just too obviously a 'big' problem to worry about defining just how big it is ;). - Benjamin Good from email
Ami Iida
“Dry water” could make a big splash commercially                   http://portal.acs.org/portal...
"An unusual substance known as “dry water,” which resembles powdered sugar, could provide a new way to absorb and store carbon dioxide, the major greenhouse gas that contributes to global warming, scientists reported here today at the 240th National Meeting of the American Chemical Society." - Mickey Schafer
Graham Steel
'Key Alzheimer's findings questioned' - NatureNews 24th Aug 2010 http://www.nature.com/news... #neuroscience
1.alz.jpg
"When Stephen Strittmatter discovered an unexpected link between key proteins in two devastating brain maladies — Alzheimer's disease and Creutzfeldt–Jakob disease (CJD) — researchers in the field agreed that he was on to something big. But a year on, conflicting results, including findings published in Nature this month, have clouded that rosy picture and highlight the challenge faced by researchers seeking a way to arrest Alzheimer's disease progression". - Graham Steel
arg: "Animal models are particularly contentious, he notes, because there is no single model that is universally perceived to be the best system in which to study the disease. And because each lab has invested its time, effort and reputation into its particular model system, this is unlikely to change, he adds. A consortium organized by the Cure Alzheimer's Fund, based in Boston,... more... - Mickey Schafer
Iddo Friedberg
Improbable Research: How to Write a Scientific Paper - http://improbable.com/airchiv...
"Scientific papers are an important, though poorly understood, method of publication. They are important because without them scientists cannot get money from the government or from universities. They are poorly understood because they are not written very well" - Iddo Friedberg from Bookmarklet
"The journal editor will pick the referee most likely to be offended by your paper, because then at least the referee will read it and get a report back within the lifetime of the editor..." - Ruchira S. Datta
"Nominally, science involves discovering something new about the universe, but this is not really necessary. What is really necessary is a grant." - Daniel Mietchen
Iddo Friedberg
Ruchira S. Datta
"Random shotgun sequencing...recovered a genome fragment from a novel archaeon, named WTF-1." http://apps.ornl.gov/~pts...
From 2006, but I just ran across it. - Ruchira S. Datta
lol, awesome. - Mitch Skinner
Ruchira comes back. - Ami Iida
Ami Iida
DRINKING WATER PROVEN TO HELP WEIGHT LOSS http://news.discovery.com/human...
Ami Iida
Spouses do not grow more alike, study finds http://news.msu.edu/story...
Next up: Do people grow more similar to their dogs? - Eric Jain
Dogs resemble their owners. - Ami Iida
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