one you will write, that explains the slides in more detail ;-) - Bora Zivkovic
Ok-will do- the videos are supposed to be on the site today, but wasn't loading for me - Christina Pikas
Christina - Nice project! I'd be curious to know if you included mathematical blogs in your study? In my opinion, they are some of the most interesting around, yet they seem to form their own little world, mostly cut off from the rest of the science blogosphere. Were they maybe a separate cluster? - Michael Nielsen
using the spin glass community det algorithm - they fell in with physics and CS (CS blogs were more like theoretical, math-heavy...). I definitely had a bunch of math blogs by both grad students and professors... They weren't completely cut off... - Christina Pikas
This is fantastic and fascinating work, Christina. Loved the note about the cluster of female bloggers talking about work climate, and dearly hope you follow it up. - D0r0th34
What is the best place to link to your post and slideshow on the SO'09 wiki? Your session is not about blogs, really, but there are a couple that are - one about networks, for instance. People should see this before coming to the conference. - Bora Zivkovic
Did you find any graph theoretic cliques? - Andrew Lang
@Andrew - tons of cliques (maximal complete subgraph of 3 or more nodes), tried also LS sets, Lambda sets, k-cores..... many of the standard cohesive subgroups in Wasserman and Faust - there too many so not informative. Unlike the typical sparse network, this network is a hairball. - Christina Pikas
@D0r0th34 - I'd love to, even had sketched it out as a diss idea, but *really* want to stay away from gender and all that, and it's a slippery slope. @Bora - not sure where to link it from, maybe start a generic page on what we know about science blogs? - Christina Pikas
Up-and-coming parts of Eastern Europe (Latvia, for example) may be surprising and enlightening in a changing world - Joe Davison
Me, too. Last year: London, Cambridge, Trieste, Belgrade, Berlin. This year I hope for a repeat of Belgrade plus some other places if I can, e.g., Stockholm, Amsterdam, Barcelona....any meeting there where I can get invited? ;-) - Bora Zivkovic
Stockholm and Berlin (let me know if you come to Berlin). - Björn Brembs
I've always wanted to do the Dalmatian coast and the Adriatic. And Spain. - Chris Cotsapas
Chris, on business extensively to the UK, France (mostly Paris), Switzerland (mostly Basel), Germany, Holland, Belgium, Spain (Madrid), Italy (Milan, Trieste, Venice) and I am sure I am missing some. With my wife, Vienna is the only place we've spent enough time. I've been to France and the UK for non-work a few times - Deepak
Just to clarify, this is for a weeks vacation :) - Deepak
several friends have been to Croatia recently and raved. Pictures were amazing... - Andrew Su
Pierre, Barcelona is definitely on the short list - Deepak
Cities: Praha, Firenze, Roma, Lisboa, Istanbul - Alain Pierrot
Deepak - put it this way. Where else in the world can you stand on a 2000 year old pavement in a building which is pretty much still standing except Bath...on the other hand England in May...bleark! - Cameron Neylon
From the list of places which you haven't yet visited, I put another vote on Barcelona. - Pawel Szczesny
if it is late May you can go midnight golfing in Trondheim, Norway :) - Amund Tveit
Cameron, Exactly. I have been to England too often in May :) - Deepak
City-vacation: definitely Barcelona (or Amsterdam, but for entirely different reasons) Hiking, outdoors and nature-scenery: - come visit Norway as Amund says - we've got fjords, mountains and lots and lots of isolated strange local people. - Nils Reinton
Living here most of my life, I wonder what people find appealing in Poland ;). - Pawel Szczesny
+1 for Norway! Studied there for a while - absolutely amazing country. Love the coast and the fjords... - Victor / Mendeley Team
+1 for Norway, and you could add Sweden and Denmark too. One option is the Öresund, Copenhagen Malmö, Lund, Roskilde, Helsingor (=Hamlet's castle), Gothenberg etc. They're all fairly close, so travel isn't difficult. - Bob O'Hara
Oh, and the Tallinn/Helsinki idea (include Tartu too!) is good. I live in Helsinki, so I might be biased. - Bob O'Hara
Good point Chris :) Deepak, feel invited to Poland, if you plan to make the Tour de FriendFeed. - Pawel Szczesny
@Chris: Excellent ! :-) Deepak, I can be your guide in the garden of Versailles :-) - Pierre
You're always welcome to visit Hungary. I'm ready to be your guide. :) - Berci Mesko
lol ... that would be fun wouldn't it. I shall present options to the boss and see what she has to say. I miss my 10-15 weeks a year in Europe (from a few years ago) - Deepak
The list above from Alain Pierrot has most of my favorites but I would substitute Lisbon with Porto (Oporto) and add Berlin. If you do go to Portugal tell me in advance and I can give you some tips. - Pedro Beltrao
@Deepak re: england in May - to be fair the last few years summer has been the first two weeks of May... - Cameron Neylon
But seriously if there is a work angle on this and you want to hook up some talks or visits then drop me a line (or hassle me at Science Online). - Cameron Neylon
Growing up in Yugoslavia, I spent every summer on the Croatian coast, so for me that is "the norm", but spatially and temporally removed now I agree that it is stunningly beautiful, especially the islands. - Bora Zivkovic
Having spent 5 days in Italy, specifically Sorrento and Capri, as well as Rome, just this last spring, I would love to return there. So much to see, so much good food and people. - Bob M. Montgomery
via twhirl
At last someone said Italy! Venice, Rome, Sorrento, Florence, Padua, Sienna - all more wonderful than anywhere? I have never been to Bali or Vigata (Sicily) where Gianrico Carofiglio and Andrea Camilleri, respectively, set their books, but I would love to visit them. - Maxine
Go to the non-Paris part of France! Auvergne! Midi! Provence! May is just before the annual influx of loud Dutch and British tourists take over the areas. - Eva
If I'm still in the country by then, you should definitely come by Lisbon, Portugal. Otherwise I may just as well need a tour of Seattle if I'm near by :) - Ricardo Vidal
Eva ... lol. One reason for going in May, although looks like I might be in Europe for conferences in March ... hmmm - Deepak
Ricardo, if you make it here, just holler - Deepak
A shortage of donated brain tissue is hampering research into diseases such as Alzheimer's, Parkinson's, and dementia, a team of British scientists warned yesterday (Jan. 6).
About 10,000 brains are used for scientific research in the UK. But researchers say that they need thousands more fresh organs from donors with both diseased and healthy brains. There are currently only 20 brains to study autism and 30 brains to research Alzheimer's in the country.
"There's a great opportunity to facilitate important research to discover cures and treatments which would go
unfulfilled if we don't increase the number of brains available for research," said Paul Francis, a neurochemist at King's College London, at a press conference in London. - Alexey
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Califano: computational scientists should spend more time learning about the biology to some extent and vice versa - will produce higher impact research - Shirley Wu
Trey Iddeker: In-house integration of computation + bio vs. straight collaboration where the two are pretty separated? Depends. - Shirley Wu
Russ Altman: agree for the most part but behoove us not to overlook the algorithm for the biology or vice versa. If there is a good biological question you should see it through, and same for the algorithm. Wary of pressure being placed on young researchers now to excel in two areas. Rather expect them to be good in one area and know how to collaborate. Will lead to faster career and research advancement - Shirley Wu
Larry Hunter: quoting Marcy McClure - "Bioinformatics is getting new science out of other people's data". Biology, success is all about creating new data. So it's hard to convince others of validity of Marcy's view. - Shirley Wu
Learn how to think like a biologist. Doesn't mean you need a lab. Just get some intuition. Learn a very small slice of biology really well and develop methods to study that biology really well. Then you can move on. - Shirley Wu
Ted Shortliffe: I'm actually going to disagree with a lot of what's been said - Sorry I'm an interloper, was actually at another meeting prior to now. Russ: "Call security!" - Shirley Wu
(By the way, I didn't catch it but I believe the question they are asking is "advice to those entering the field" or something of that nature)_ - Shirley Wu
being good in the two areas (lab+maths/computer) is not really easy. These are very different mindsets and I know of very few (actually maybe just one) PIs that actually have working experience on both. - Pedro Beltrao
Ted Shortliffe: Need to have a love and appreciation for the informatics. These methods could have really broad applicability (not just biology or medicine) but they get overshadowed by the flashier biology - Shirley Wu
Great discussion. Wanting to like this twice. - Neil Saunders
Califano: Could be really valuable to treat biological systems as informatics systems to glean new insights. COmputational scientists think about experiments differently, can be useful to think about it their way - Shirley Wu
Idekker - wants to see bioinformaticians get more involved in the planning of experiments or studies. Analogy to EMT called to scene of accident trying to piece together what happened - Shirley Wu
Audience member: collaboration is easy if you're a big name, but much harder for most of us. Even if you have a great tool, really hard to find an experimental lab willing to test it. Claim: need a different type of experimental science or we need to make our own - Shirley Wu
Russ Altman: depends on choice of problem you're trying to solve, and planning in advance. Might be unfair expectations/pressure for experimentalists to get out of the blue request. Choice of problem - what if you have great algorithm but no existing dataset to do "rediscovery" type validation? It helps to have a plan at the outset for validation for it to be successful. - Shirley Wu
califano: you could turn it around. Experimentalists come to informaticians all the time and say "i have this microarray dataset, can you help me analyse it?" So we need to be diplomatic, learn each others' language, invest time and effort in collaborations up front - Shirley Wu
One problem with that is that in many cases , top-down research leads to biological predictions that can be related to many different fields so it is not easy to plane in advance for collaborations. - Pedro Beltrao
Shortliffe: experience of bioinformatics students going to work in wet labs that have never had a bioinformatics student before. Mindset of wet lab at the beginning is "great, I have an IT techy person to help out now". But the good students transform the lab's thinking, show them what bioinformatics research can really do. Point is that students, not full professors or big names, CAN have a big impact in people's attitudes - Shirley Wu
Idekker: observes that to get faculty positions in good bio programs you need to have familiarity with computational tools. So attitudes are definitely changing - Shirley Wu
Question: suppose collaboration is successful. Then what? What do you do with the data? Where do you publish? Is there a bias against the methods/bioinformatics approaches in top journals (e.g. cell/nature/science)? - Shirley Wu
Idekker: yes there are examples of papers where the bioinformatics methods or analyses or even results are in the supplementary table 7.2.a. But also examples of papers where the bioinformatics really made the paper. It's our choice. - Shirley Wu
Russ Altman: "you say you have a great result." Is it a great biological result? or a great informatics result? Use this to determine where to publish. Chip Lawrence's Gibbs sampling paper in Science as example of how the informatics result was THE important. - Shirley Wu
Hunter: could also try publishing two separate papers to highlight the two different aspects of the research. Doesn't have to overlap that much or count as redundant. Both are important. - Shirley Wu
Audience followup: So then you hav Nature papers and Nature Methods papers. What about when someone looks at your CV and they say "we wish you had more Natures and less Nature Methods". - Shirley Wu
Shortliffe: well, who are you trying to impress? informatics people or biochemistry people? Depends on the field too - you could publish a hugely important method which won't be in a big impact factor journal but a ton of people will read it and reference it because it's really useful - so you've had a huge impact on the field if the field is small - Shirley Wu
(hmm, more tension between the establishment (IF) and more heuristic types of credit and evaluation) - Shirley Wu
Russ Altman: even if you have a million Nature papers as middle author, you will be asked what was your contribution, and that's what matters. Fewer Nature papers but more important contributions will go farther. - Shirley Wu
Steve Brenner asks panel: At biology conferences, the panels revolve around how to the protocols work, the results, analyses, etc. At bioinformatics conferences the panels (and especially here at PSB) they talk about "how do we do our science better" - Shirley Wu
Oh, when are we going to stop ranking ourselves using glamour mags? - Neil Saunders
Russ Altman: "can you say some more about what the biology folks talk about?" Steve: "you know did you put reagent X in solution Y, etc, things that are -". Altman: "Trivial" - Shirley Wu
"people who are faint of heart should not enter this field because the boundaries are unclear, constantly being defined, etc" If you want more well-defined boundaries then go into a more traditional field - Shirley Wu
Hunter: show of hands - who is in an actual "bioinformatics or medical informatics department"? (small smattering of hands) "And most of those were probably founded by Ted (Shortliffe). So you're not being judged by your peers." which is part of the problem. - Shirley Wu
Shortliffe: telling a story about Russ Altman (Shortliffe was faculty when Russ was an applicant for the MSTP program at Stanford). Russ was interviewed by one of the current students on the applicant selection committee. - Shirley Wu
Student summarized Russ's case by saying "when he was at harvard he was in a great lab, but when you talk to him today, he has this interest in computers which kind of worries me but I believe in his heart when he gets here he will do great science." Reflecting that back then and even now, fighting to defend that what we're doing is science, mixing computer science with biology. - Shirley Wu
Russ: "as you can see, I tricked them and it worked". - Shirley Wu
Steve Brenner: rhetorical question. "if what we're facing is endemic to the nature of our discipline, are there models of other disciplines that have come before us that we can use as a template rather than having to pave our own way?" - Shirley Wu
Califano: Corollary to genetics? Almost all the other disciplines if you think about it have been revolutionized by computation. In the future, expect to have all experiments in silico first. - Shirley Wu
Hunter: likes to use biostatistics as model. Methods development, ethos of service and collaboration, considered successful and so it's possible. (ed. Not sure if i like that example) - Shirley Wu
Ideker: would welcome discussion about methods, results, analyses, rather than ethereal meta-discussion. Suggests Steve Brenner plant questions in audience at bioinformatics conferences in that vein to redirect disucssions when they drift towards the meta-discussion. - Shirley Wu
Question about funding. How to sell our research effectively, etc. Driven by the funding to pursue specific problems when our methods could be applied to many different things - Shirley Wu
Hunter: huge investment in health information technology infrastructure coming up. HIPAA is a lesson for what can happen - collateral damage to research enterprise. What aspects of health technology infrastructure do we need? - Shirley Wu
Sean Mooney: lots of investment in information cyber-infrastructure too. CTSA awards, etc. Comments that informatics is not getting any easier - how hard is informatics going to get as these systems come online, as storing and recording data get more complicated? - Shirley Wu
Russ: agree, it is getting harder. Example with next-gen sequencing. We thought we had it all under control, we have BLAST, etc. but then next gen sequencing came along and all hell broke loose and everyone is scrambling - Shirley Wu
Battery running out about now, so will go quiet but I will try to take paper notes and transcribe - Shirley Wu
Audience: informatics types like things well-defined. this works ok with molecular functions, but not with diseases - hard to define phenotypes, molecular basis, etc. Where is the unification of ontology/definition w/disease so we can bring in effective informatics for clinical applications? - Shirley Wu
Target the biology of HIV, which requires use of host cell machinery - need to predict novel direct physical interactions between HIV-1 and human proteins. - Shirley Wu
Dyer et al Bioinformatics 2007, Davis et al Protein Science, Konig et al Cell 2008 previous work. But no study doing global analysis - Shirley Wu
Supervised learning. Dah, that slide went by too fast. HIV-1 and human protein pairs represented with set of features - Shirley Wu
Use decision trees, random forest classifier with majority vote out of possible trees - Shirley Wu
Training and test data taken from keyword search of proteins and relationship terms. Differentiated between direct relationships ("binds to", "acetylates" etc) and indirect ("regulates", "affects") - Shirley Wu
35 features including expression data, PPI data, sequence motifs, etc - Shirley Wu
motif example: does human protein contain ligand domain or belong to ligand protein class? does HIV protein contain binding signature? - Shirley Wu
Also use similarity of HIV-1 protein to human protein's interaction partner - sequence, cellular localization, post-translational modifications, etc - Shirley Wu
evaluation: AUC 0.92 and Mean Avg Precision 0.23. - Shirley Wu
Results recapitulate observation that pathogens tend to interact with host proteins with high degrees of connectivity to other proteins - Shirley Wu
Resulting predictions: Tat interacts with Pin-1? - Shirley Wu
I'd be a bit surprised if that were true, since a quick look at Tat sequences in GenBank indicates that it contains only one consensus Pin-1 recognition motif (ser/thr-pro), and the thr at that position is not well conserved (it's not, for instance, present in the refseq). - Bill Hooker
Also, Tat is one of those miserable proteins (small, charged, ?globular) that will *interact* with pretty much anything. Whether the interaction means anything is another matter. The NCBI Gene entry for HIV-1 Tat lists well over a thousand protein-Tat interactions... - Bill Hooker
I didn't really catch it hence the question mark. It was definitely Tat interacts with something, which doesn't really help - Shirley Wu
"“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
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Is the field of bioinformatics in trouble? I ask this due to two disturbing trends. The first is the misuse of bioinformatics for "dubious" purposes. The second is, has bioinformatics itself reached a wall of stagnation due in part to disciplinary insularity and resultant inadequate collaboration with its medical counterpart? - Paulo Nuin
In "A Professor and an Anti-Aging Tonic", Roy Poses commented on an academic who misused bioinformatics to violate the trust of patients and also violated their trust by getting entangled with commercial interests, in this case with what seems a magic potions operation. - Paulo Nuin
Bioinformatics appears to receive more media attention and offer more status, career opportunities, and compensation than the less-prestigious medical informatics. - Paulo Nuin
This is exactly the issue I raised in my Merck letter. I fear in the field of Bioinformatics, this occurs frequently, and in fact billions of investor dollars are going down the drain in the pursuit of cybernetic in-silico miracles as a result. - Paulo Nuin