Jennifer Gardy › Likes

Ruchira S. Datta
I'm here and will be attending the BioPathways SIG. I figured there should be some place to say non-talk-specific things like "I've arrived!", so here it is. - Ruchira S. Datta
Will be switching between DAM, BOSC and the BioPathways. Once I've figured out which talk is when ;) - Oliver Hofmann
Uhoh. I sense a lack of places to recharge notebooks. This is going to be fun during the session breaks.. - Oliver Hofmann
I forsee a problem with the SIG posts in FF - only one heading, and many, many speakers.... Hopefully will be OK for people following. - Allyson Lister
The projectionist kindly suggested I power up in the projection cubicle during the coffee break. - Ruchira S. Datta
Network is slowing down to a crawl for me. - Oliver Hofmann
Sitting at home, following the conference. Great job folks! My only wish is that there was some place where the speakers would upload their presentations. - Lars Juhl Jensen
Help! Anyone got a UK plug adaptor with them I could borrow for an hour or so? Will happily exchange laptop charge for beer/coffee. - Cass Johnston
Oliver, I've been having that problem too. There were some times when I had posted a comment and wanted to post another one, but the first hadn't finished posting, so I had to wait for the post to finish, hold my comment in my head, and also pay attention to what the speaker was currently saying... - Ruchira S. Datta
Talked to the organizers. They are aware of the problem, IT is looking into increasing bandwidth. Yay. - Oliver Hofmann
@Oliver well done! Perhaps we could ask someone to look into more power extension leads? :) - Allyson Lister
Anyone up for a FF lunch / dinner / drink at some point during ISMB? - Oliver Hofmann
Sounds good. I'm about to go orienteering, though, so will be out of reach this evening... - Ruchira S. Datta
Monday and Tuesday are the only "free" nights, with poster sessions going from 5:45 to 8:30 pm. Shall we just set Monday night for the FF meet-up? When would people want to leave the conference at the earliest? 8 pm? - Michael Kuhn
Monday's going to be busy meeting everyone; I'd probably try and stick around 'till 8pm. Meet at the registration booth close to the entrance at 8:15? Can decide on a venue depending on our numbers and whether people are willing to travel to the city center. - Oliver Hofmann
I think I would prefer 8:40. I have a poster. I haven't figured out yet whether it's Monday or Tuesday, but others might have posters too? Last year, at least, I was explaining my poster to people pretty much constantly until the poster session closed. - Ruchira S. Datta
Monday or Tuesday is good for me - either way, and any time is fine. It's a good idea! - Allyson Lister
8:45 on Monday then, same place (registration area)? Do we have any locals with suggestions? - Oliver Hofmann
ok - see you all in registration at 8:45 monday :) - Allyson Lister
If everyone has already seen Gamla Stan by that time, we could go to Södermalm--plenty of good restaurants. I'm staying there. - Ruchira S. Datta
@Ruchira: works for me as long as we have a guide to get us there :) - Oliver Hofmann
@Allyson There are lots of power extensions along the windows just inside the T hall. Let me know if those are still too full and I'll see what I can do about getting more. - Dave Messina
@Oliver The conference organizers have bought high-speed internet. Anyone can go to the registration desk for a free login. Spread the word! - Dave Messina
@Dave, yep, got mine this morning. World of a difference. - Oliver Hofmann
@Dave, any chance of getting extension cords to the other conference rooms? Starved for outlets at K21 :) - Oliver Hofmann
I'll be arriving today, would it be worth to pack a extension cords with multiple sockets? - Roland Krause
@Roland: This is always a good idea. Problem is that some rooms only have power on the stage and in the projection booth. - Michael Kuhn
Organizers also have extra extension cords for emergencies, but even the main conference room has no outlets. Best to recharge during the breaks, but that means leaving the notebook unattended... - Oliver Hofmann
photos from ISMB/ECCB, please put on flickr under tag "ismbeccb2009" - Burkhard Rost
The projectionist here just unplugged my power cord from their outlet and said none of us will be allowed to use their outlet; we'll need to use the outlets in Hall C. He said the organizers did not pay for extra outlets, so we will still have this power problem. - Ruchira S. Datta
Well, at least I'll be able to sit closer to the front where I can see better. - Ruchira S. Datta
Even the "free" network is considerably faster and more responsive today. Well… we'll see what happens when the first coffee break hits. - Johann Visagie
@Ruchira: Ouch. That's not going to help. We can get extension cords and use them in the smaller meeting rooms though. - Oliver Hofmann
@Johann agreed - I also think the network is faster today - Allyson Lister
I love the fierce, ofttimes violent competition for the limited resource that is power outlets during coffee break! - Johann Visagie
It seems a simple #ismb is the twitter hashtag of choice. Also note Burkhard's suggestion above to use "ismbeccb2009" as Flickr tag. (Hey! Flickr tags can has spaces! ;) - Johann Visagie
@Johann: Bring your own socket multiplier and you are loved by everyone ;-) - Oliver Hofmann
Any chance of leaving / recharging our desktops at the registration desk during the breaks? Would rather not leave mine in a conference room unattended. - Oliver Hofmann
Lonely FFer near the registration desk is looking for some chatting... anyone? - Egon Willighagen
Sure, I'll wander by momentarily. - Ruchira S. Datta
I'm sitting on the ground in front of the registration desk, waering a black t-shirt... - Egon Willighagen
Any poster presenters here on FriendFeed? Maybe you can start a new post in the ISMB/ECCB room and attach your poster PDF? - Egon Willighagen
Great idea, Egon! Not being at the conference, I would very much appreciate being able to see some of the posters on FF. - Lars Juhl Jensen
Lars, are you in Stockholm? - Egon Willighagen
What about special sessions, I do not see them here. - Diego M. Riaño-Pachón
I'm having a special FF sessions outside, but I am the only participant :) (after a nice meet up with Ruchira earlier) - Egon Willighagen
@Egon - shame - I was offline for lunch. At least I assume it was lunch you said that. FF doesn't put up the time each comment was made - so add times please if you're talking about meetups! Hopefully see most of you this evening after the poster session anyway :) - Allyson Lister
P.S. The network seems to have slowed down again. Anyone else notice, or is it just me? - Allyson Lister
@Dave thanks for the power extension cable - except for the main victoria hall (as we discussed) it's really helped a lot :) - Allyson Lister
@Allysin, I'm still around... in front of E.A.T. now.... - Egon Willighagen
@Egon - ah, but I'm in a talk! :) - Allyson Lister
@Egon, no I decided not to go this year - Lars Juhl Jensen
@Allyson: As half of the conference is probably sharing the username / password for the closed network I am not surprised it is slowing down :) - Oliver Hofmann
Maybe it is because I am happily uploading Jmol 11.7.45 to SourceForge ? :) - Egon Willighagen
@Allyson Glad to help! - Dave Messina
@Oliver Hopefully it's that rather than someone downloading Genbank. :) Still plenty of FREE logins for the closed wifi are available at the registration desk for anyone who wants one. - Dave Messina
Fun to see how quickly many of us have found a workaround for the 'Oops'... :) - Egon Willighagen
Is there a place for posting jobs/student positions available to ISMB attendees? (i.e. I'm not at the ISMB this year, so am definitely checking out FF and related resources and thank you all for your posts! - Fiona Brinkman
Does anyone know how to 'filter out' all group:ismbeccb2009 messages in my main feed? So that I can just open the ISMB/ECCB 2009 group in a separate window? - Egon Willighagen
Thanks to everyone - organizers, reviewers, presenters, friends, bloggers etc etc etc : I must away, but had loads of fun! :) - Allyson Lister
@Allyson, safe travels. @all, see you in Boston. Feel free to PM/mail me for tips where to stay, eat or party in the city. - Oliver Hofmann
nice meeting you, Allyson, and have a safe trip! - Ruchira S. Datta
I am leaving too, was nice meeting you all and have a good trip back. - Roland Krause
Conference finally closed. - Peter Menzel
i'm now at the Stockholm airport en route to Cambridge for another conference (!) It was fun meeting some of you and microblogging together. Hope we'll see each other around at future conferences. Next year in Boston! - Ruchira S. Datta
@Egon: if you go to the ismbeccb09 room and click the "(edit)" link to the right of "Lists" then you can deselect it from your Home feed. - Lars Juhl Jensen
A top-ten of talks (well, not really - just the top ten of my ISMB posts based on number of hits). What was everyone interested in enough to click through to my blog? Find out: - Allyson Lister
Oliver Hofmann
SIG: Short-Read: Bayesian mixture models for detection of SNPs in ovarian cancer transcriptomes, Sohrab Shah
Workflow for clinically relevant variations: alignment of reads, detection of variants (focus of the talk), confirmation of SNPs and distinction between somatic and germ line changes, annotation of SNP with frequency, functional significance etc - Oliver Hofmann
Pprobabilistic graph model with 3 states, obviates the need for depth-based thresholding - Oliver Hofmann
Fits model to data using EM - Oliver Hofmann
Expanded model takes mapping / base-call qualities into account - Oliver Hofmann
16 ovarian cancer transcriptomes from samples with different clinical outcomes. Identified recurring FoxL2 point mutation in granulosa cell tumours, not found in 800 other cancers. - Oliver Hofmann
I wish one of my methods would lead to a NEJM paper. Hooray Sohrab! - Jennifer Gardy
Iddo Friedberg
M3 SIG: Tom Matthews, Pathogen Profiling Pipeline
A series of reductive sets.: BLAST to refset --> assign hits --> calculate equivalent hits --> clustered BLAST and filtering - Iddo Friedberg
Last Common Ancestor estimation: sounds like the same algorithm as MEGAN - Iddo Friedberg
remove host contamination by BLASTing against the host and removing the 100% hits from those - Iddo Friedberg
Looks like a very solid pipeline. No URL given. Tom Matthews is from the national health center of Canada. - Iddo Friedberg
The NML (National Microbiology Laboratory) is basically Canada's CDC. They did some great swine flu sequencing work recently. I'm very impressed with this pipeline. Very impressed indeed. - Jennifer Gardy
Iddo Friedberg
M3 SIG: Eric Alm, MIT. A fine scale genomic map of early history of the planet
Do modern genomes show traces of ancient geological events? - Iddo Friedberg
AnGST algorithm: reconciling gene trees with species trees - Iddo Friedberg
OK, he's actually doing automated phylogenomics. But not calling it that by name (if I understood correctly) - Iddo Friedberg
Reconciliation constraints: no grandfather paradox - Iddo Friedberg
Robinson Fold score: something I need to check out - Iddo Friedberg
wow. He shows a correlation between times of abundance of oxidizable metals, and those genes that use them. Or at least those genes that are involved in oxidative pathways. This is cool. - Iddo Friedberg
Ruchira S. Datta
BioPathways SIG: Daniele Merico, "Enrichment Map: A novel visualization method for gene-set enrichment analysis results"
Gene Sets, Pathways, and Networks. - Ruchira S. Datta
Enrichment analaysis is performed on gene sets, e.g., after clustering of gene expression data. - Ruchira S. Datta
Test over-representation using Fisher's exact test or hypergeometric test. Or may use alternative null hypotheses. - Ruchira S. Datta
Gene sets are interrelated by overlap. Enrichment map plots these relationships as a network. - Ruchira S. Datta
Applied to breast cancer cell signaling pathways: estrogen 3 receptor. Found e.g. cluster related to cell proliferation. - Ruchira S. Datta
Edge thickness represents amount of overlap. - Ruchira S. Datta
GO hierarchy has three components; enrichment shows different kinds of relationships. - Ruchira S. Datta
Nodes are colored red for upregulation and blue for downregulation; size indicates number of genes in the geneset. - Ruchira S. Datta
Apply to disease signatures of genotype-phenotype studies. - Ruchira S. Datta
Instead of color coding up/down-regulation, might map cluster analysis or principal components analysis results. - Ruchira S. Datta
Can demote pathways to gene sets and run enrichment maps on them. - Ruchira S. Datta
Enrichment maps can be used as an entry point for more detailed pathway-level analysis. - Ruchira S. Datta
Can put in pathways and networks and re-organize using enrichment maps. - Ruchira S. Datta
Have free Cytoscape plugin. Download from here: (website currently under maintenance). - Ruchira S. Datta
Using too many gene sets may result in clusters that are too dense, making the map hard to navigate. - Ruchira S. Datta
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