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ISMB 2008
For anyone interested in following ISMB 2008, Toronto. Arrange meet-ups, micro-blog the talks and whatever else you like.
The official room for ISMB/ECCB 2009: http://friendfeed.com/ismbecc...
Daniel MacArthur, Mickey Kosloff, Anne Tuukkanen and 12 other people liked this
This year, ISMB will auto-generate posts for each talk around 10 minutes before the start of the talk, so that the live-blogs can be linked to the ISMB homepage. I hope we'll have lots of coverage!
- Michael Kuhn
ISMB will also advertise this on their homepage and in the conference newsletter, so hopefully we'll get many new contributors.
- Michael Kuhn
Only 4 days to go! Would love to be there and catch up/meet new faces, but vicarious participation via copious microblogging will be the next best thing :-)
- Neil Saunders
Will we be able to micro-blog the SIGs from this room as well?
- Allyson Lister
Yes, no problem. We will generate posts for each SIG meeting.
- Bettina
@Bettina - thanks :)
- Allyson Lister
This doesn't look like a room - it's actually a "friend", even though it's a conference "friend". Is this because you don't want people starting topics there? As it stands, we'll only be able to comment on existing topics, and not post interesting links etc EXCEPT as they relate to an already-started topic. Perhaps this is deliberate to keep things on-topic. Is this what you were going for? Just curious... :)
- Allyson Lister
you're right, I didn't realize this. I brought it to the attn of the admins. It might be deliberate (because of the integration with the ISMB website), but then one should probably create another room to coordinate meet-ups etc.
- Michael Kuhn
Thanks, Michael. Yes, the idea was to keep it more organized. We will create another room for the "ismbeccb2009-talk" where everyone is welcome to post but please use the official "ismbeccb2009" conference room for all discussions regarding the presentations (Highlights, Proceedings Track, Technology Track, SIGs and Keynotes).
- Bettina
@Bettina - thanks for the reply. While I'm not 100% sure that splitting things up like this will work (people might not switch that much between the two), I can see the reasoning and hope it works well. Perhaps these reasons should be added to the taglines of the ISMB "friend" and the ISMB talk group you mentioned, so that when people go to one, they see both what it's for and how to get to the other one... Thanks! :)
- Allyson Lister
Ok, its true, switching between groups might not work. I talked with my supervisor and we decided now to change the settings. So now everyone of you should be able to post in the ismbeccb2009 room.
- Bettina
@Bettina - thanks, looks good. Looking forward to the start of the conference on Saturday! :)
- Allyson Lister
After talking with Reinhard Schneider, one of the ISMB09 organizers, I opened a new room to try to begin the discussion how to integrate the ISMB homepage with FF/microblogging in general. I hope we can find some low-tech solutions with the help of the FF API and widgets. - http://friendfeed.com/rooms...
Roland Krause, Neil Saunders and Cameron Neylon liked this
ISMB 2008 report - http://docs.google.com/Doc...
Daniel Jurczak, Lars Juhl Jensen, Deepak Singh and 2 other people liked this
OK, this open doc could be used to collect ideas for the report. If you want to contribute, please leave a message here, preferably with what you would like to add. For now, the document only contains some scribbles and nothing of general interest.
- Roland Krause
I have now added the first notes on the literature mining results to the document. I will try to make a figure out of it tomorrow - just a simple plot showing the growth of the terms that I have found.
- Lars Juhl Jensen
I've added a draft of my writeup for the Web 2.0 BoF. Feel free to edit!
- Shirley Wu
Just to make sure everyone notice: I have gone through out manuscript and made a few comments. I think the manuscript is in a quite good shape, so we should be able to finish it quickly once we are all over the NAR database deadline on September 15 :-)
- Lars Juhl Jensen
I added a (draft) small report on the BioPathways SIG. I can trim it down to fit as a box or maybe it can just go in supplementary I don't really now. I will check the main article tomorrow.
- Pedro Beltrao
Added few subtle changes to FriendFeed collage.
- Daniel Jurczak
Can I get access to it? I am on the Short Read way.
- Steve Wu
ISMB 2008 selected abstracts: Tweet Cloud - http://www.tweetclouds.com/user_pa...
And 2007: http://www.tweetclouds.com/user_pa...
- Neil Saunders
ISMB 2008 = highest profit/participant, as mentioned proudly by the chairman. He assures it's not because of the food, that they are actually spending quite a bit on the food. Maybe it's being delivered to the wrong place.
Kuan-Ting Lin, Antonis, Jason Stajich and 3 other people liked this
What I heard is that the number of paper submissions was down by 30%.
- Paulo Nuin
can anyone tell me why the espresso machine at the convention center breaks down every moment precisely when i need it most?
- Shannon McWeeney
Paulo: So is the amount of free t-shirts. Conincidence ? ;)
- Daniel Jurczak
we paid $435/head for food and coffee, the conference center+AV+MCC related costs amounted to another about $180/head. you do the math how much of your money went into food. totally with you on your surprise, but it is actually the same for most places in the world we went to; some were much worse than toronto, others much better (e.g. vienna). - espresso machine: another one of those things: i for one need good espresso: you guys have no clue what the MCC would have charged for 'second cup' quality ..
- Burkhard Rost
In Detroit there was no included food and in some days there was almost no place close to the GM Centre with good food (if you call Detroit's greektown a place that you can get decent food ...) and the registration price was adequate. Why include food in the registration when some people cannot afford it? Like me, unsupported post-doc living in Toronto. No way I am shelling 775 (700 reg + annual fee) plus whatever the BOSC costed and eat moderately bad food.
- Paulo Nuin
Does the chairman think high conference profits will encourage even more people to come next time?
- Duncan Hull
The ISMB is a community effort and the organizers thereby responsible to the community to organize a financially viable meeting. I am glad that Burkhard is as bold as to discuss this issues in public. Organizing a conference is a multi-optimization problem that should have higher weights on scientific content, adequate conference rooms and WLAN (in that order) than food quality, which were met at this years' ISMB for sure.
- Roland Krause
Some conferences do not provide lunch at all (e.g. the genetics congress in Berlin in July), but for Stockholm, this is probably not an option (fair ground).
- Roland Krause
IMO, good conferences do make a profit, always tough for scientific ones. But the logistics and experience better be worth it then.
- Deepak Singh
no lunch is what i have been proposing since years; will become stronger on this! for Stockholm: too late (and yes too difficult); for Boston 2010: we already signed the contract including food, however, we will try our best to get out of it; for 2011 in vienna: difficult - upside: that's perceived as "good food"
- Burkhard Rost
profit: half of the ISCB annual budget originates from the ISMB profit, we need $180K from ISMB to survive; we now run ISMB at an incredibly ambitious low budget saving wherever we can, this is one reason why Toronto will create high profit/participant - mostly due to the fact that we cut on organizing costs. still the major issue remains that we pay for the facilities that could welcome 1000 more participants and with every new participant we would profit more. put differently: we have to grow or to shrink
- Burkhard Rost
Was that "paper submissions down by 30%" true? $550 - 900 per person. 1000 attendee. Let's say... 30% on foods: $300 X 1000 = $300,000 for lunch and matrix party. Foods must be delivered to the wrong place.
- Kuan-Ting Lin
see our paper in PLoS CB on ISMB 2008 about numbers, although the following may not be in there: vienna proceedings submission=492, toronto: 292; ok; NOW please realize that this has absolutely NOTHING to do with costs! One issue: we had over 180 talks at ISMB 2008; 48 were from proceedings=less than 1/3. now the money: food/head was over $400 NOT 30%!!! there were over 1400 participants and the food was way more than 2* your estimate; matrix party was cheap! food & rent for Liberty Grand was a lot.
- Burkhard Rost
Hey folks, ISCB almost died from less profitable meetings in Brazil and Australia...give Burkhard a break. I like his openness. Yes, the food could have been better (the box lunches at the Member's meeting during lunchtime were really good!), but I didn't see enough affordable restaurants on Front Street or near the CN Tower to handle us all. I do agree that when possible, letting us...
more...
- John Greene
In Vienna (that is if it is again at the Vienna International Center) it is not that easy to get to food. I mean there is nothing in the immediate vicinity. Additionally as Burkhard already mentioned the food there was actually quite fine. Anyway, i appreciate the openness of the discussion here.
- Daniel Jurczak
ISMB 2008 report by the organizers (PLoS Computational Biology) - http://www.ploscompbiol.org/article...
Neil Saunders liked this
Seems to be more preview than review? Anyway, useful for us so we can avoid too much similarity in our report.
- Neil Saunders
Aye.
- Roland Krause
note the date: was written BEFORE ISMB, i for one am not good enough to devine "reviews" - we invite you guys to write reports about the meeting and send them to BJ to coordinate where they will go
- Burkhard Rost
ISMB News - http://www.iscb.org/ismb200...
Lars Juhl Jensen, Pawel Szczesny, Roland Krause and Deepak Singh liked this
"ISCB is looking for a few aspiring reporters, who also happen to be attending ISMB 2008 in Toronto. (...)This year we are also seeking a select corps of students and Jr. Scientists to take on the role of writing about the vast scientific content of the conference and the personal experience of participating in this large, international bioinformatics event. Submissions will be reviewed for posting to the ISMB website, and will be considered for publication in the designated ISCB pages of PLoS Computational Biology, the Society's official journal, as a single author report or as part of a larger report compiled from the contributions of multiple authors."
- Pedro Beltrao
via Bookmarklet
Hmm, shouldn't we (the ususal suspects) grab the bull by horns and write a decent conference report, compiled from multiple sources?
- Roland Krause
I'm up for some reporting, once my brain has adjusted :)
- Neil Saunders
folks: another one of those: spent a lot of energy in vain hoping to get something similar to what you guys pulled off: totally impressed!!! Thanks. write it up, we'll put it onto our journal pages if we'd find it ok. other than that: we'll like a blog at a central place in stockholm and will link to this one as soon as steven leard is back from his deserved break. burkhard
- Burkhard Rost
Hi Burkhard , I am glad you find this experiment interesting. It ended up being a useful way not only to gather notes about the conference but to set up events on the fly. It would be great to have something like this set up from the beginning at the next ISMB.
- Pedro Beltrao
Just add my voice to the fact that I think this was really impressive grass roots reporting. I felt like I was actually at two meetings at the same time, one where I was physically present, and one where I was just a fly on the wall. Great example of what can be done (with enough people and the right tools)
- Cameron Neylon
again: have tried to find you guys before; now that i found you i will do whatever i can to support this for future ISMBs; let me give you another impression: i saw the blog for the first time during the wed morning keynote, after the keynote i stood up and thanked Lars & Neil (those were the ones i had seen in the 20 secs i spent on this); at least 30 people walked up to me after that announcement and asked how to get at that blog!
- Burkhard Rost
Thanks Burkhard! I think that it would be a great idea to improve the visibility of the live blogging from the official ISMB web site. However, it is also important that we don't try to formalize it too much as this would likely kill a grassroot effort like this. I find that FriendFeed worked remarkably well (much better than my personal attempts on Tumblr), so I suggest that we try to stick to that but somehow tie it in with the ISMB web site.
- Lars Juhl Jensen
One possibility would be to set up an ISMB2009 room ahead of the conference and prefill it with one thread per presentation. These can then be used to comment on each talk. By making them ahead of time, we could link to the thread in an iframe on an official ISMB page with the speakers abstract. This would allow people to work in an almost unchanged manner, yet it would structure the comments slightly better and hook it up with the official web site.
- Lars Juhl Jensen
Another wild idea: virtual poster sessions. Could we somehow get people to upload a high-resolution bitmap of their poster? These could then again be linked with a FriendFeed thread to allow commenting. Perhaps the posters could even go on Flickr and be fed directly into FriendFeed?
- Lars Juhl Jensen
Roland & Neil, I'm also up for helping out on writing a conference report. Burkhard, where would the conference report be published - in PLoS Comp Biol or Bioinformatics?
- Lars Juhl Jensen
Lars, we are in touch with BJ Morrison. There is a Googledoc with 5 minutes worth of scribbles by me but I wonder whether a fresh start - or sketch - wouldn't be advantageous. 2000 - 5000 words, I guess, the rest is up to us. Oh and yes, PLoS Comp Bio.
- Roland Krause
Roland, excellent - can you email me an invitation to join the Googledoc? I can try to take a look at it later today.
- Lars Juhl Jensen
Hi Burkhard - I've been on the road since ISMB, just got back to this conversation. I'm glad you found the FriendFeed coverage valuable and I think we're all looking forward to contributing again at future ISMBs.
- Neil Saunders
neil: you did not see this because you had obviously left already; i saw your feed first on wed. morning; i stepped up after hannah's talk and announced it and was bombarded by questions: 'how to find that' for the rest of the day, literally at least 20 people approached me. Will anybody write for journals?
- Burkhard Rost
ISMB 2008 Conference Proceedings now available on-line at: http://bioinformatics.oxfordjo... - http://www.iscb.org/ismb200...
Pardon me. I don't get it. Where's the proceeding?
- Kuan-Ting Lin
Thanks
- Kuan-Ting Lin
FYI: proposed to FF to place a comment link at the bottom, and other things we missed at ISMB - http://groups.google.com/group...
Neil Saunders, Roland Krause, Pedro Beltrao and 2 other people liked this
Tuesday's circle of laptops - http://friendfeed.com/e...
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Lars Juhl Jensen and Cameron Neylon liked this
the images are rather noisy, so only low-res versions :(
- Michael Kuhn
Does anyone know, whether the live video feeds of each presentation they are streaming to the iMacs next to the Biomed Central stand are recorded in any way ?
Deepak Singh liked this
Went to the information desk and asked. People there were surprised to hear that there even is a videocast. So even though, from a technical point of view, everything is in place, there is no recording.
- Daniel Jurczak
ISMB sent me a fax to sign to allow them to record my talk and to make derivatives such as videos that would enhance a publication. My talk is for the PLoS track so I assumed that it was for them to record the talks to add to SciVee.
- Pedro Beltrao
cool
- Daniel Jurczak
1) glad you liked it; was my idea and a hell of work; 2) no recording because (i) everyone else felt this is too low quality, (ii) actually, not that simple to record what is streamed is it?
- Burkhard Rost
Flickr: "ismb2008" - http://flickr.com/photos...
Cameron Neylon liked this
some pictures from ISMB2008 (sorry for the duplication)
- Pedro Beltrao
want to put up a web site with many photos from ISMB 2008: anyone to help?
- Burkhard Rost
We're putting together a conference report but would like to include the more "human" side of things. If you have funny stories, anecdotes, speaker quotes, reflections, or would like to contribute, just encapsulate it in 1 para or less and we'll fit in as many as we can. Paste here or link to it.
Pedro Beltrao liked this
great: let ISCB know, we'll link to it!
- Burkhard Rost
Conference hack: Embracing the backchannel at Start - http://www.veen.com/jeff...
Pedro Beltrao, Deepak Singh and Roland Krause liked this
the Start conference will have an ombudsman following twitter/IM/email to give the audience a voice. nice idea.
- Michael Kuhn
HL 24: eQED
Pedro Beltrao liked this
Initial Example Yeast QTL strains
- Shannon McWeeney
"Genetical Genomics" integration and analysis of genotyping and expression to identify regulators
- Shannon McWeeney
Reviews common problems: large genetic regions, multiple hypothesis testing, and that complex trait composition applies to regulators as well (multiple regulators potentially of small effect and with redundancy)
- Shannon McWeeney
Integration of physical interaction data - with idea that it will give us true regulators. If we have 10 genes in locus, true regulator should be closer wrt network distance than others to target gene. random distribution of others (not sure if i agree with that- could be other types of correlation)
- Shannon McWeeney
Need scoring to rank interactions and identify true regulator
- Shannon McWeeney
Simulation (based on idea of communication as electric current). weak confidence equivalent to high resistance etc.
- Shannon McWeeney
Note: score all pathways not just most likely
- Shannon McWeeney
Computational Fine mapping example. reference was knock out expression data in yeast. 550 associations between regulator and target gene. random accuracy =22%. Tu et al random walk 48%, shortest path 64% eqed 72%
- Shannon McWeeney
Integrating several e-qtl loci. Idea similar to epistasis that main effects may not be significant but joint effects are important. Inclusion of genes not significant but which connect loci
- Shannon McWeeney
Important point: several e-qtls that reinforce same part of the network. ability to mine integrated information
- Shannon McWeeney
Q: wouldn't bayesian networks be more natural approach rather than circuit with constraints
- Shannon McWeeney
Q:how were weights define? Prob based on confidence of PPI. Also ability to exploit correlation in expression
- Shannon McWeeney
ismb2008 - Twitter Search - http://search.twitter.com/search...
Archive of twitter hash tag #ismb2008 - you could try just "ismb" too
- Neil Saunders
via Bookmarklet
I am leaving soon, thanks to everyone that participated. It was a fun and interesting experiment. See you "around"
Daniel Jurczak and Michael Nielsen liked this
You're flying out today?
- Paulo Nuin
yeap, around 6pm today
- Pedro Beltrao
Too soon, we barely talked. Have a safe trip back to California.
- Paulo Nuin
I am also on my way to Pearson, it was nice meeting you all (Pedro, Shirley, Neil, Roland..).
- Daniel Jurczak
Nice to meet you all as well, it looks like I missed some good sessions/keynotes, but the FF coverage was great!
- Shirley Wu
It was great to meet you all! I missed all the talks, but thanks to the FF coverage, I at least have a pretty good idea of what I missed ;-)
- Lars Juhl Jensen
Great to see everyone, finally. Safe trips home to you all; I'll be back in Brisbane (and online) August 5.
- Neil Saunders
Keynote 8: David Haussler - "100 million years of evolutionary history of the human genome"
Jason Stajich, Adrian Heilbut, Frank and 3 other people liked this
Here we are at the big finale
- Neil Saunders
It has been fun :)
- Pedro Beltrao
october to end of November each year submissions of names for awards
- Pedro Beltrao
Lab homepage http://www.cbse.ucsc.edu/staff...
- Pedro Beltrao
Very, very long introduction to the speaker
- Neil Saunders
The application Powerpoint has quit unexpectedly :)
- Neil Saunders
reconstruction of genome evolution. looking at segment duplications and genome evolution. Second trend - trying to unite the different scales of genome evolution from large scale re-arrangements to point mutations.
- Pedro Beltrao
the slides are not working but he is doing a good job of improv
- Pedro Beltrao
ah the slides are back
- Frank
Jiam Ma, Bernard Suh and Brian Raney, work on evolution of history of a mammalian chromosome (rat)
- Pedro Beltrao
Showing rat chromosome X as example of evolutionary changes
- Neil Saunders
Duplication and integration graphs that would make nice wall decorations too
- Roland Krause
Evan Eicher- Morpheus: new genes by segmental duplication. Is Morpheus a tool ? No, it is a gene.
- Pedro Beltrao
Morpheus (Evan Eichler) - new genes by segmental duplication
- Neil Saunders
The demise of a acyltransferase 3 by a stop codon in the chimp/human lineage. The last protein of that particular fold
- Roland Krause
Second example: gene loss; mutation to stop codon before the human-chimp branch
- Neil Saunders
zooming in to single base reconstruction , mutation to STOP condon for a gene in the divergence with orangutan (~15My)
- Pedro Beltrao
Reconstruction of evolutionary history of placental mammals
- Neil Saunders
project for the community : reconstruct the evolutionary history of genomes (totally agree that this is going to be exciting, I am interested in having this information for ascomycota, I think Ian has nice tools for this)
- Pedro Beltrao
Nicely illustrated with photos of mammals next to the tree
- Neil Saunders
Genome evolution: infinite sites model; covers (1) speciation, (2) duplication and (3) break/rearrange; shows some breakpoint graphs
- Neil Saunders
the infinite sites model of genome evolution - 2-breakpoint rearrangements (different groups use this)
- Pedro Beltrao
2-breakpoints rearrangements - pair the 4 ends together randomly
- Roland Krause
Reusing breakpoints - intractable problem for >= 3 genomes; explains how to get around this by not using same breakpoint twice
- Neil Saunders
Neutral drift, negative selection, positive selection all now recognisable for multi genomes
- Neil Saunders
The new method looks interesting but I could not keep up with it. something about using all positions instead of breakpoints in many more genomes to reconstruct the ancestral states.
- Pedro Beltrao
~ 5% human genome under negative selection
- Neil Saunders
Some regions might change from negative to positive selection. Search for human accelerated regions (of positive selection ?) Har1 example
- Pedro Beltrao
Mentions the HAR1 gene (human accelerated region); conserved structural RNA; specific expression in developing cerebral cortex; expressed with cortical development protein Reelin
- Neil Saunders
I'm glad I stuck around for this talk - beautiful stuff
- Adrian Heilbut
collaboration with Pierre Vanderhaeghen http://dev.ulb.ac.be/pvdhlab/ to experimental test the role of HAR1 in human brain development
- Pedro Beltrao
Where and how do functional RNA structures arise ?
- Pedro Beltrao
Moving now to ultra-conserved regions; ~ 500 000 in human; example - cluster of elements near ARX gene shown to act as enhancers (lacZ fusion)
- Neil Saunders
It's a fantastic combination of hard math and soft biology (embryonic development)
- Roland Krause
Elements absent from invertebrates; how do so many appear relatively quickly? links this to transposons
- Neil Saunders
Talking about their work on ultra conserved regions, Experimental tests for these regions (expression patterns). Many ultra-conserved regions but all arose recently (evolutionary time). How can these all be created so rapidly ? possibly due to some form of transposon mediated copy
- Pedro Beltrao
One such ancient transposon strongly matches coelacanth - how cool is that!
- Neil Saunders
comment: the evolution of vertebrates was facilitated by transposons
- Pedro Beltrao
The grand challenge: The reconstruction of the evolutionary history of each base of the human genome (applause)
- Roland Krause
Again, the grand challenge of human molecular evolution is to be able to reconstruct the evolutionary history of each base. (it really shows that he is passionate about evolution :)
- Pedro Beltrao
Hmm; he almost goes with the "mammals at top of the ladder", but then takes a step back.
- Neil Saunders
And that's it. Let's understand the history of mammals through their genomes.
- Neil Saunders
question: are the evolutionary breakpoints related to cancer breakpoints ? general response - the breakpoints are re-used so maybe
- Pedro Beltrao
SS07: The future of scientific publishing - The publishers view
Michael Habib, Rafael Sidi, Duncan Hull and 2 other people liked this
Uh oh, no slides "unstructured digital publishing"
- Roland Krause
Matt Cockerill (BioMed Central), Claire Bird (Oxford University Press), Catherine Nancarrow (Public Library of Science)
- Michael Kuhn
PLoS, BMC and OUP
- Roland Krause
MC: quality control function of scientific publishing; peer-review can be a rate-limiting resource for sharing scientific knowledge; need efficient process; will see more sharing of reviews between journals
- Michael Kuhn
MC: reviews should separate soundness from how exciting the research is
- Michael Kuhn
Validation processes
- Roland Krause
MC: medical community more open to open peer review than biologists, might change (Biology Direct)
- Michael Kuhn
Open peer review - the Matt Cockerill mentions medical journals and Biology Direct
- Roland Krause
Matt Cockerill talked about re-using reviews from higher impact journals to lower impact journals, talked about lower tier (PLoS ONE and BMC Notes), open peer review (works in medicine and Biology Direct)
- Pedro Beltrao
much more information structured, needs open access
- Pedro Beltrao
Fast talkers and slow internet connections
- Roland Krause
MC: would be nice to have full text so that more meta-analysis can be performed
- Michael Kuhn
CB: expects to see new networks and tools that can complement impact factors
- Michael Kuhn
Claire Bird ... quality of data and re-usability of the article is important and integrity of the publishing process needs to be sustained. community will decide the limits of usefulness of a publication.
- Pedro Beltrao
Catherine Nancarrow - alternative peer review model ? self-organizing community online. How comments , ranking etc could be counted for career progress
- Pedro Beltrao
CB: is there an alternative to the current model? Discussion recently: self-organizing communities on the web [hmm, didn't Nature try this?]
- Michael Kuhn
Question by Pedro: We can't find out currently how many people download a paper. MC: Publishers recognize this, think about how to share access data; perhaps fully open citation base [Thomson won't like this]
- Michael Kuhn
Q: Cooperativity and data-sharing – author lists and order is an incentive against data sharing; "support" scientists don't get the credit they deserve; perhaps author list in alphabetical order would be more egalitarian. CN: Require author contributions in the meta-data. Strive to be as transparent as possible. MC: With the right collection of data, these "hidden" contributions could be measured
- Michael Kuhn
Peter Karp - maybe we could have an ontology of contributions (sounds interesting)
- Pedro Beltrao
Q: Perhaps we could have an ontology of contributions? Or the author contr. could be aggregated
- Michael Kuhn
Reactome developer - it has been very difficult to have Reactome tracked in Pubmed.
- Pedro Beltrao
Q: someone from Reactome; complains that it took a long time to have the database listed in PubMed; is there a way to make this more visible [didn't fully understand this] MC: Interested to talk to UniProt guys, current tools are drived towards journal articles, but they should also track DBs
- Michael Kuhn
Discussion about Open Access (not really about publishing on well)
- Pedro Beltrao
MC: NIH repository policy might lead to freely accessible publications, which are still under restrictive licenses (re: text-mining)
- Michael Kuhn
Nucleosome Positioning Signals in Yeast and Human Genomic DNA. - William S Noble
Daniel Jurczak and Neil Saunders liked this
aside: scatter density plot is a nice way to show a dense scatterplot
- Adrian Heilbut
I remember this guy from a blog post on SVMs at Flags and Lollipops
- Neil Saunders
Noble is probably the most important advocates of SVMs in bioinformatics. The middle initial stands for SVM I think (in times like this)
- Roland Krause
SS07: The future of scientific publishing - G. Cesarini on Structured Digital Abstracts
A project underway at FEBS Letters in collaboration with the MINT data base
- Roland Krause
Large gap between articles on PPI and publications of low throughput experiments
- Roland Krause
started working in structured information due to experimental work going on in the lab. Explained the creation of MINT and the iMEX consortium. The annotation by curators are not covering no-where near enough the increasing number of pubmed articles
- Pedro Beltrao
The principle of structured digital abstracts (SDA) http://www.febsletters.org/article...
- Roland Krause
Project started in January, first issue (see above link) in April 2008
- Roland Krause
Link to press release with useful information http://www.eurekalert.org/pub_rel...
- Pedro Beltrao
The authors can reject doing the structured abstract, I think this is where it might fail, if most people don't want to do it.3 in 4 accepted .. not bad, only 30 structured abstracts so far. 16 out of 30 authors filled a survey about the process.Some points: 1h of average time to do it. 6/10 had some difficulty. the most difficult task was the find the uniprot ID (wow). 2/16 said that this could affect their decision to publish there again
- Pedro Beltrao
161 articles published, 30 with SDA
- Roland Krause
90% wrong assignment on taxonomy
- Pedro Beltrao
The data is almost insignificant in relation to the whole field but the information int he FEBS experiment will be useful for publishing world.
- Pedro Beltrao
The general problem so far has been that authors make mistake so curators still have to spend considerable time on the process. Pubmed did not accept to add the structured abstract to the Pubmed abstract.
- Pedro Beltrao
in the future they hope to have more journals participating and more types of information captured (they focus on articles that describe protein-protein interactions)
- Pedro Beltrao
SS07: The future of scientific publishing - Mark Gerstein on text mining to study the structure of science
Neil Saunders, Michael Nielsen, Daniel Jurczak and 3 other people liked this
Introduction: the rapid growth of databases and publications
- Roland Krause
Blurring the distinction of databases and journals, particular in biology as a fact based science
- Roland Krause
distinctions between databases and journals are blurring
- Michael Kuhn
New Vision: Science 2.0: studying the structure of publishing
- Roland Krause
science 2.0 == science about science (??? wouldn't that be meta-science ???)
- Michael Kuhn
Science 2.0 as the science of science ( I don't think I agree with this definition)
- Pedro Beltrao
Seeking a New Biology through Text Mining, Andrey Rzhetsky; http://www.cell.com/content...
- Michael Kuhn
Web mining: extract simple statements, find new information.
- Roland Krause
Structure of science: Co-authorships, subjects
- Roland Krause
Seringhaus et al., Chemistry Nobel Rich in Structure, http://www.sciencemag.org/cgi...
- Michael Kuhn
Mashups: Search for nobel prize by subject http://www.ncbi.nlm.nih.gov/pubmed...
- Roland Krause
using text mining to understand the structure of science, how ideas evolve, etc (the net is not great here). highly studied genes, knowledge bias. I think Valencia has been one of the first to show this.
- Pedro Beltrao
Would also be easier to follow a less productive scientist
- Roland Krause
Uncovering trends in gene naming; Michael R Seringhaus et al; http://genomebiology.com/2008...
- Michael Kuhn
comparing literature nane over-representation with something like google search rank for gene names. Not surprisingly the names that are more abundant in "human discourse" than in literature are "funny" names that already exist.
- Pedro Beltrao
comparing name co-authorship graphs in different institutes (that is an interesting idea .. it would be interesting to do this for different science topics)
- Pedro Beltrao
Structure of co-authorship networks in relation to consortia to identify bias in selection of targets for structural genomics projects
- Roland Krause
mapping science topics as whole (I did not get the name of the authors for this)
- Pedro Beltrao
Giving the example of RNAi where the birth of the field is captured in the databases. Clusters of co-authorship graphs over time
- Pedro Beltrao
The impediments to the vision of a connected way of scientific publishing
- Roland Krause
Federation rather the centralization
- Roland Krause
getting to the idea of structured abstract. Involving the authors in the production of a machine readable abstract for the work.Saying that even a small set of structured abstracts could be used as gold standard.
- Pedro Beltrao
Notes the absence of a social framework for protecting data on the web
- Roland Krause
social framework for the protection of papers and data on the web. We don't know how to regulate data sharing online. a legal problem that needs to be resolved.
- Pedro Beltrao
Lots of interesting lectures on the subject at http://lectures.gersteinlab.org/
- Roland Krause
HL53: Chen-Hsiang Yeang - "detecting coevolution in and among protein domains"
Slight title change - protein/RNA sequence, rather than domains
- Neil Saunders
Starts with overview of coevolution and methods: parametric (Bayesian, Markov) or non-parametric (mutual info, correlation coefficients etc). First type incorporate phylogenetic information, but overfitting and cost are issues.
- Neil Saunders
Figure showing generalised CTMP model for coevolution
- Neil Saunders
This looks very applicable to things like protein-peptide interactions
- Neil Saunders
Showing how to construct sequence substitution rate matrices for 2 sites
- Neil Saunders
First example: looking at 16S rRNA structure to predict interacting pairs; comparison with 4 other models - CO, WC, WCW, MI; CO model best AROC.
- Neil Saunders
Now moving to tertiary interactions in rRNA; also works well
- Neil Saunders
Now moves onto protein domains; screening of Pfam database
- Neil Saunders
1.2 x 10e11 all v. all possible pair comparisons
- Neil Saunders
Showing some statistics that describe co-evolved domains
- Neil Saunders
Coevolving pairs of sites are spatially coupled (shorter pairwise distance - but not necessarily in contact)
- Neil Saunders
Examples to illustrate: Fe/Mn superoxide dismutase; first protein structure that I've seen all conference :)
- Neil Saunders
Second example: ribosomal proteins; coevolving positions are at tRNA binding sites
- Neil Saunders
Skips through RNAP (similar to ribosomal story) to phosphoglucomutase: the coevolving positions are in functionally-important regions
- Neil Saunders
Wrapping up: coevolving sites in RNA often physically interact; not so in proteins. Software is freely available: www.sns.ias.edu/chyeang
- Neil Saunders
HL49: Ian Holmes - "Transducers"
A probabilistic framework for modeling indels on phylogenetic trees
- Neil Saunders
This is a method from computational linguistics finding application in bioinformatics
- Neil Saunders
Some example apps: Ortheus, SAPF, Indelign, GConstructor, Tree-HMM - and several more
- Neil Saunders
Nice animation of evolving DNA sequence showing substitutions, indels, duplications - TKF91 model
- Neil Saunders
Transducer is stochastic finite-state machine; very similar to pair HMMs, but slightly different probabilistic output (conditional)
- Neil Saunders
Second animation shows string transducers on a tree
- Neil Saunders
Scales poorly - states increase exponentially with taxa; various ways around this (monte carlo HMM, Gibbs sampling)
- Neil Saunders
Phylocomposer - uses Graphviz to visualise transducers in various contexts: e.g. alignment, trees; allows design of your own operations
- Neil Saunders
HMMoC (HMM Compiler) - automated generation of code in C++
- Neil Saunders
Benchmarking statistical alignments (BAliBase) - improvements over e.g. Clustal using affine-gap transducers.
- Neil Saunders
Also applicable to RNA structural alignments
- Neil Saunders
It's all at biowiki.org
- Neil Saunders
A questioner says RNA clustering by structure is "the simplest clustering problem he ever did" :)
- Neil Saunders
SS07: The future of scientific publishing
Thomas Lemberger, Neil Saunders and Michael Kuhn liked this
Robert Murphy: Mining images and caption from the scientific literature
- Roland Krause
Images should be understandable without the text
- Roland Krause
Examples: different colours, blank fields (information!), non-regular grids, graphs and images in the same grid
- Roland Krause
(missing due to slow connection)
- Roland Krause
Hand label, supported by machine learning, store in data base. Recognize scale bars, type of image, find the references between caption and figure.
- Roland Krause
SLIF: Subcellular location image finder http://murphylab.web.cmu.edu/service...
- Roland Krause
Interrogate the database by protein, location, cell type, resolution, GO terms, etc.
- Roland Krause
Future: more automated system, improve practices for defining figure contents in papers.
- Roland Krause
Mentions the Elsevier journal contest
- Roland Krause
Future: Structured digital caption - hidden XML tags, includes coordinates, panel label, panel type, annotations, scale and length units
- Roland Krause
Use of multilayer figures should be included with archival XML
- Roland Krause
Very interesting work creating value, certainly underused
- Roland Krause
The presentation is available too http://murphylab.web.cmu.edu/present...
- Roland Krause
Keynote 7: Hana Margalit - "intriguing roles for small ncRNAs in cellular regulatory networks"
Hsuan-Cheng Huang, Ricardo Almeida, Samuli Eldfors and 2 other people liked this
Focusing on post-transcriptional regulation of expression by small RNA
- Neil Saunders
~ 85 sRNA known from E.coli; targets and function often unknown, but often conserved
- Neil Saunders
miRNA regulators in eukaryotes: mechanism still unclear (inhibition/degradation/both)
- Neil Saunders
> 500 miRNA in humans; also conserved; also few targets or functions known
- Neil Saunders
Comparing sRNA regulation to other types; transcriptional, PPI
- Neil Saunders
Modelling and simulation of regulation: regulator may be (1) always expressed, (2) switched on by external signal
- Neil Saunders
sRNA regulation advantageous where fast response required
- Neil Saunders
Next: how does this integrate with transcriptional regulation?
- Neil Saunders
Finally, someone provides a clear, succinct summary of what a network interaction graph is
- Neil Saunders
Where 2 TFs required, feed-forward loop = AND gate
- Neil Saunders
May be mixed loops: combination of ncRNA and protein factors
- Neil Saunders
Example mixed feed-forward loop: OmpR + MicF (sRNA) -> ompF
- Neil Saunders
Other examples known in bacteria and human
- Neil Saunders
Mixed negative feedback loops: e.g. RyhB -> Fur, E. coli; stochastic simulation.
- Neil Saunders
Summary: mixed regulation extends possible regulation dynamics
- Neil Saunders
Moving onto predicting miRNA targets in genomes
- Neil Saunders
Use known targets to narrow the solution space; miRNA "seed region"; conservation at target site; repeat binding sites
- Neil Saunders
RepTar algorithm: starts with 3'-UTR, HMM profiles repetitive signals, matches to miRNAs
- Neil Saunders
Validation using shuffled sequences and experimental data; not over-selling the method
- Neil Saunders
Predicted miRNAs: seed match (84%), 3'-compensatory (11%), nearly-full match (5%)
- Neil Saunders
Moving on to applications of RepTar: viral miRNAs
- Neil Saunders
Significant overlap of predicted targets for different viruses: GO annotations make sense
- Neil Saunders
Second set of targets are immune system-related; do viruses use miRNA to down-regulate immune system?
- Neil Saunders
HCMV: evades NK cells by mimicking MHC-I to make cell appear "self"
- Neil Saunders
MICB - top target for HCMV miRNA UL112; experimental validation by over-expressing UL112 in cell lines; MICB down-regulated, controls are not. Also use luciferase reporter assay with 3'-UTR and mutagenesis of binding site.
- Neil Saunders
Viral infection of UL112 deletion mutant confirms results
- Neil Saunders
Describing further experimental confirmation. Obviously quite excited about her results :)
- Neil Saunders
Viral miRNAs may therefore be therapeutic targets; e.g. for antisense RNA, or mimic miRNA effect for immunosuppression
- Neil Saunders
Great talk. Wrapping up now - running through almost to 10 am.
- Neil Saunders
Good coverage too, Neil
- Roland Krause
Wow, the Neil Saunders one-man show :)
- Lars Juhl Jensen
PT47: BLASTing Small Molecules - Statistics and Extreme Statistics of Chemical Similarity Scores. Pierre Baldi
Deepak Singh and Neil Saunders liked this
why is there no equivalent to BLAST for small molecules? is there a fundamental difference between small molecule similarity and sequence similarity? (PB think that seq. alignment even works for non-evolved seq., I tend to disagree --> site-directed mutagenesis!)
- Michael Kuhn
It's a good question. I guess small molecules are defined by structure, rather than linear chains of letters. They should still be searchable though.
- Neil Saunders
reviews fingerprint method; standard approach: Tanimoto
- Michael Kuhn
can come up with different chance models for fingerprint matches
- Michael Kuhn
Given the diversity in tautomers, conformers, the variety in R-groups, etc, it's a different problem, IMO
- Deepak Singh
[Huh, can't liveblog if the battery is empty]
- Michael Kuhn
based on the ratio between two Gaussian distributions (one for the union and one for the intersection), can get p-values / Z-scores / e-values for a particular database
- Michael Kuhn
evaluation: 55 known estrogen receptor binders x 100,000 random (presumably negative) compounds from ChemDB do leave-one-out tests on probability to get a false positive. Can fine-tune this to fingerprint size.
- Michael Kuhn
[Editorial remark: I think this is very important work. However, I'm skeptical that it is a good idea to use biased chemical libraries for such analyses. For sequence BLAST, your standard is the genome which is under evolutionary pressure. Chemical libraries are not under such pressures, and therefore you can get "significant" hits in your database that are due to uneven sampling of the...
more...
- Michael Kuhn
Blast is acting on only a 1D string... There are many, *many* ways to define the similarity between molecules (see a review I wrote http://dx.doi.org/10..., but much more literature around). There is so much more complexity in small molecules than a amino acid sequence. Think if it as loop modeling for protein, but then without the luck of pinpointing the loop start and end to some homology modeled tertiary structure.
- Egon Willighagen
Still, sounds an interesting read. Did Baldi mention a paper, maybe?
- Egon Willighagen
yes, this is in the ISMB proceedings: http://www.ncbi.nlm.nih.gov/pubmed...
- Michael Kuhn
Michael, thanx!
- Egon Willighagen
Keynote 6: Bernhard Palsson - "systems biology: an era of reconstruction and interrogation"
Hsuan-Cheng Huang, Burke Squires, Deepak Singh and 7 other people liked this
PA plays "don't let the sun go down on me"...
- Neil Saunders
systems biology of human metabolism
- Roland Krause
Kicks off with an iphone joke :)
- Neil Saunders
Who would start with an iPhone joke :) ?
- Pedro Beltrao
1. paradigms 2. Links and nodes (network bioogy) 3. Maps and functional states 4. Workflows and knowledge bases 5 Reconstruction 6. Human reconstruction of the metabolic network 7. Application
- Roland Krause
Talk outline looks mighty ambitious
- Neil Saunders
components, networks, models, phenotypes (the paradigm)
- Roland Krause
omics to knowledge base to in silico modeling to validation and discovery
- Pedro Beltrao
Systems biology: components -> networks -> computational models -> phenotypes
- Lars Juhl Jensen
Conversion of biochemical data to query-able format
- Neil Saunders
1. maps to database, 2. knowledge base 3. query tools 4. validation and discovery of missing parts, synthetic biology
- Roland Krause
So, his paradigm for sysbio maps to a large, structured and detailed knowledge base
- Roland Krause
Various levels of modelling; detailed chemical kinetic knowledge the most specific
- Neil Saunders
general property of cells - prototypical transformation are bi-linear.
- Pedro Beltrao
Molecular biology links are fundamentally bi-linear, e.g. bimolecular reactions and interactions
- Lars Juhl Jensen
Network links constrained by chemistry
- Neil Saunders
Metabolic networks cannot be randomized for statistical evaluatiuon - no pyruvate will go to isocitrate just so.
- Roland Krause
relative rates are fixed by thermodynamics but absolute rates are highly variable inside the cell. General comment, links are very constrained by the physical attributes of the nodes. Interesting comment about problems in creating a random network with little knowledge of atomic information.
- Pedro Beltrao
Can now visualise pathways in context of entire metabolic network
- Neil Saunders
nice thing about genome scale models is that we can look at pathways in the context of the whole model. "Pathways are models networks are reality" Uwe Sauer
- Pedro Beltrao
Analogy between road maps and traffic (functional states) and biological networks. Getting closer to flux balance analysis
- Pedro Beltrao
Network topology fixed, but functional states vary constantly - nice analogy with traffic on highways through the day
- Neil Saunders
Cobra suite http://www.ncbi.nlm.nih.gov/pubmed... (a recent in Nature Protocols)
- Roland Krause
contained based models work also because evolution creates systems that are optimized for some function. It is not easy to know what are these functions that are optimized.
- Pedro Beltrao
COBRA software available as Matlab package
- Neil Saunders
OK, vectors and matrix operations, sysbio at last
- Roland Krause
I hope he does not say biblioome
- Pedro Beltrao
Moving on from fluxes and matrix operations to workflows + knowledge bases; mentions EcoCyc as example
- Neil Saunders
@pedro uwe sauer (eth)was the author of the pathways quote
- Ildefonso Cases
Tables: rows are metabolites; columns are reactions; must be balanced (like balancing reactions in high school, but larger scale); you then map this to the metabolome as well as you can
- Neil Saunders
@Ildefonso thanks
- Pedro Beltrao
Metabolic reconstruction 1. Genome annotation 2. Model to perform tests (gaps etc) 3. Simulation, 4. Validation (go back to 2. if problems arise).
- Roland Krause
The human metabolic and regulatory network is 10k by 15k today
- Roland Krause
Feis 2008 Nature reviews Microbiology (new review on the subject) I don't think it is available
- Pedro Beltrao
Showing plot of available genome-scale reconstructions over time
- Neil Saunders
An idea for community effort for 2D annotation. Example of yeast reconstruction jamboree, accepted in Nature Biotech (out in a few months) Slamonella/Klebsiella jamboree September 2008
- Pedro Beltrao
Talking now about community annotation efforts; kind of like hackathons
- Neil Saunders
Annotation jamborees to come: Salmonella and human (in 2008)
- Roland Krause
2 years , 7 people to build the human metabolic network from literature 1134 genes, PNAS.. He could have mentioned another human reconstruction that was published in MSB
- Pedro Beltrao
RECON 1 knowledgebase - is it available somewhere?
- Lars Juhl Jensen
Dimensions: 3D (ultrastructural reconstruction); 4D - states over time
- Neil Saunders
3D reconstruction of transcription in E. coli - spatial and temporal aspects of the network
- Roland Krause
Last topic - what can we (the audience) do with reconstructions
- Neil Saunders
"ask not what you can do for your reconstruction but what the reconstruction can do for your" ... phenotypic behavior, network analysis, bacterial evolution, metabolic engi, biological discovery. (http://www.nature.com/nbt...)
- Pedro Beltrao
Ask not what you can do for reconstruction - Ask what reconstruction can do for you
- Lars Juhl Jensen
Uses: metabolic engineering; evolution; network analysis; phenotypic behaviour; discovery (missing parts)
- Neil Saunders
A lot more people working in these type of models. Mentions recent paper by Barabasi (http://www.ncbi.nlm.nih.gov/pubmed...)
- Pedro Beltrao
Prediction of missing reactions or even missing pathways
- Lars Juhl Jensen
Knowledge gaps: reactions, metabolites
- Roland Krause
Covering some uses of the RECON 1 knowledge base
- Neil Saunders
@Lars, I think Recon 1 is a reference to that human model in Duarte et al PNAS, and I think it is all available.
- Pedro Beltrao
Q10 synthesis gaps http://www.ncbi.nlm.nih.gov/pubmed...
- Roland Krause
@Pedro, that is also how I understand it now :-)
- Lars Juhl Jensen
co-sets - Using metabolic networks to predict the cause of SNPs (concept MSB paper 2006). several examples of how SNPs associated with phenotypes that could be predicted by the network. Mentions again the Barabasi paper linked above
- Pedro Beltrao
Recon 1 + gene expression map to localize the map by tissue. (lost me on nthe application ) I think the reference was Nature Biotech 2008
- Pedro Beltrao
Construction of tissue-specific models by combining Recon 1 and tissue expression data
- Lars Juhl Jensen
Multi-omics data integration; basically mapping all sorts of datasets onto each other; gives example of mapping OMIM to expression profiles
- Neil Saunders
Proud to be on time.
- Roland Krause
Wrapping up. I thought it was a pretty impressive overview.
- Neil Saunders
connectivity map data set (Lamb et al); expression data mapped to recon 1 metabolic network gen set; identified metabolic signatures for 540 expr. profiles; case study: anti diabetic drugs cluster very well; can see systemic down-=stream effects of drugs; one co-set includes HMG-CoA reductase (interesting to check other targets in the co-set if they are drug targets)
- Michael Kuhn
Hypothesis: members of the same co-set should have identical effect on cell state -> implications for drug development by suggesting alternative targets
- Lars Juhl Jensen
Well done everyone - this was an awesome coverage of the talk :-)
- Lars Juhl Jensen
Yes, great coverage. Useful for me.
- Michael Barton
Web 2.0 BoF session planning notes - http://docs.google.com/Doc...
Samuli Eldfors, Roland Krause, Adrian Heilbut and 5 other people liked this
The BoF is on Tuesday from 1-2:15pm in room 718B
- Shirley Wu
Feel free to suggest or modify topics, volunteer to demo something, etc. I'm hoping this will be very interactive
- Shirley Wu
Two years ago we already talked about Web 2.0 and actually gave a talk series at EMBL. Back then, we had RSS, delicious, citeUlike, but of course not twitter/friendfeed. I actually think that (as we've proven here) FriendFeed is a really effective way of forming an ad-hoc community, so I guess we should give another talk at EMBL. :) Anyway, we should give people this link as it's a Web 2.0 introduction for scientists: http://van.embl.de/cb...
- Michael Kuhn
Hmm, I thought publishing it would make it editable by anyone but apparently not. Is there a way to do this?
- Shirley Wu
This invitation link should work for anyone: http://docs.google.com/Doc... (I hope there are no spam-bots trawling for google docs links...)
- Michael Kuhn
Cameron had an excellent blog on Friend Feed introduction for scientists (http://blog.openwetware.org/science...). I have a few other links related to the use and impact of FF on the blog (http://wildtype.wordpress.com/2008...)
- Shannon McWeeney
If someone asks about Second Life we could show them Second Nature's homepage (http://www.nature.com/secondn...) where Nature hosts talks. A good example of a recent talk was the 23&me talk (http://scienceroll.com/2008...). I don't have a lot of experience in Second Life but I don't mind flying around if the connection is good enough.
- Pedro Beltrao
One nice example of the use of second life in science is for archeology http://www.digitalhumanities.org/dh2007...
- Pedro Beltrao
Session starting now
- Pedro Beltrao
The google doc was updated as the session was going on with the gist of the discussion
- Shirley Wu
It went reasonably well. My fear is always that there will be...silence...but quite a few people contributed.
- Neil Saunders
Searching & Predicting Drug-Like Compounds Using Max Common Substructure (Yiqun Cao)
Deepak Singh, Michael Kuhn and Roland Krause liked this
it has been a while since I learned about tree search algorithms. re-reading Norvig would be good for my soul
- Adrian Heilbut
use a set of compounds as a basis to generate feature vectors; use any similarity measure you want
- Adrian Heilbut
http://bioweb.ucr.edu/ChemMin... - open, and C source available with python bindings
- Adrian Heilbut
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