Monday, July 05, 2010

Summary of #iEVOBIO Day 1 #evolution #phylogenetics #informatics #opensource

Well, just getting around to writing up some thoughts on the iEVOBIO meeting I went to earlier this week.  It was really quite excellent so here are some thoughts/notes.  Today I am writing about the background and Day 1.  Most of this is simply a catalog of what happened along with some twitter details ... In a few days I will write up a post on what I think it meant ....

The background: how I heard about iEVOBIO (skip to below if you just want to know about what happened in the meeting)  

The first I heard about regarding the meeting was Dec 7, 2009, in a Direct Message on Twitter from @rdmpage.  That would be Rod Page, who I had never met, but followed remotely via twitter, his blog, his software and his papers.  He wrote
Hi Jonathan, hope you got my email about speaking at iEvoBio in June. No pressure, just checking that it made it into your in box.
I had known about Rod for a long time since I had used his software since I was in grad school.  For example, I used to use Treeview for all phylogenetic tree viewing/drawing etc.  It seems from the history, it has been available since 1996.  Not 100% when I started using it, but it was around then.  Then I switched over to using Treeview X a few years later.  And I have used on and off some of his other software.  More recently I have followed his blog/tweets/web sites closely.

When Rod invited me, I was on a mini vacation in Monterrey and I had not actually seen his email yet (I am ALWAYS behind in reading email).  So I found the email, inviting me to give a Keynote at this cool sounding iEVOBIO meeting focusing on informatics for phylogenetics, evolution and biodiversity.  Sounded great actually.  Especially the part about Open Source:
iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software developmentand reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with arecognized Open Source License, and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial
I also liked the notion of a challenge - in this case there was a challenge for new visualization methods for evolutionary data. In summary the challenge was:
From phylogenetic trees to population networks, whether on printed pages or in GoogleEarth, visualizing evolution is a key part of our discipline. Inspired by the challenges and opportunities visualizing presents for our field, the first iEvoBio challenge is "To create a new visualization tool or platform to support evolutionary science".
Alas, since I was on vacation I did not have all my schedule information with me, so I said I was not sure. Fortunately, when I got back, it looked like good timing with the Evolution meeting just before so I said sure.

Going to iEVOBIO (skip to below if you just want to know about what happened in the meeting)

Anyway - jump to last week, skipping over some of the preparatory stuff for the meeting. I was planning on being in Oregon for almost a week, including the SSE meeting just before iEVOBIO and a meeting for my iSEEM project in Eugene before that.  But I just could not deal with being away for that long including over the weekend, after having not really taken any time off in a while.

So I went home and skipped SSE2010 and then headed back to iEVOBIO on Monday the 28th. I flew on Southwest from Sacramento to Oregon, took the light rail into the city, and walked the last bit to my hotel.  I arranged to have dinner with Aaron Darling, a Research Scientists working in/with my lab who was at SSE.  We had a good dinner and then I went back to my room and stayed up until about 3:30 AM working on my keynote talk.

I really wanted to include some new stuff and also include some background on microbes and microbial diversity and so worked very late making new slides, piecing together slides from multiple talks, and then trying to delete slides since my talk was way way way too long.  The final project I did not finish that night.

I set my alarm on my phone and asked for a wake up call and got about 3 hours sleep. I got up around 6:30 worked on my slides for an hour, and then took a showed and heading downstairs where I borrowed a hotel bike (god, I love Portland - free bikes at my hotel) and biked along the river, over the bridge, and after a little hunting around found where I could park and lock the bike.  And I went in.

I worked on my talk for another 30 minutes in an isolated corner and then went over to the main part of the conference center. Finally I was done.  I was amazed at how crowded it was.  Were all of those people there for iEVOBIO?  Alas, no - SSE2010 was still going (I did not realize it would still be on).

After asking around I found the meeting room and met the one and only Rod Page (we had never met).  I made sure my laptop would connect with their system and then headed out to get coffee - there was a Starbucks in the hallway outside the meeting room.  Alas there was a giant line and my talk was in 25 minutes.  Fortunately, Aaron Darling was in the line and he agreed to purchase a latte for me.  I went back in, made sure everything was set, and paced around until I got my coffee from Aaron and then it was time for the meeting to start.

The meeting itself: Day1 part 1: keynote by me 

The meeting kicked off with a few details from some of the organizers including Rod Page and Todd Vision.  We found out who the other organizers were (Rod Page (University of Glasgow), Cecile Ane (University of Wisconsin at Madison), Rob Guralnick (University of Colorado at Boulder), Hilmar Lapp (NESCent), and Cynthia Parr (Encyclopedia of Life).  We also found out who helped fund the meetings (US National Evolutionary Synthesis Center (NESCent), and the Society of Systematic Biologists (SSB). I am no longer sure exactly what else they said.  But there seems to have been at least one tweet about the intro:
  • toranaga Todd Vision mentions how computational biology is a guild, full of people that take great pride in their craft.
And then Rod introduced me.  Pretty funny actually.  He gave me grief for writing about bad omics words and yet inventing and then using phylogenomics for everything.  And then my talk was on.  Here it is on slideshare.

Also - there were a few tweets about my talk including the following:
I got asked some great questions afterwards including one by Joe Felsenstein, one by Arlin Stoltzfus, and one by James McInerney (well, McInerney mostly gave me grief about how he disagreed with me about the extent of lateral gene transfer).

Day1 part 2:  Short talks 

After my talk, thankfully for all involved, there was a coffee break.  And then we were back with short, ~15 min talks. These are listed below with some information, most of it from Twitter.

Day 1: part 3: Lunch - here are some tweets that came out around that time ...
Day 1 part 4: Challenge talks

And then the post lunch challenge talks began.  These related to visualization tools entered into the meeting challenge mentioned above and described here.
Day 1. Part 5. Lightning talks.   
  • dgaston83 Now time for the lightning talks. Gives me a good idea what to expect for mine tomorrow. Glad I'm on day 2!#ievobio
  • toranaga #ievobio lightening talks! 5 minutes and then the gong goes off

Day 1. Part6. Software bazaar and demos

Then there were was the software bazaar and challenge demonstrations, which alas, I skipped most of because of the lack of sleep the night before.  It seemed quite packed in there and I was just exhausted. So I went back to my hotel, riding the bike I had borrowed from the hotel back, slowly, along the river.

Here is what I missed:
  • Software bazaar
    • W. Berendsohn: The EDIT Platform for Cybertaxonomy
    • R.J. Challis: Pipefinder - semantic pipelines made easy
    • B. Gemeinholzer: DNA Bank Network Ð a virtual linkage of natural history collections' voucher specimens and documentation with physical DNA, sequences, and publications
    • M.J. FavŽ: eFECTIV: Shape analysis using elliptical harmonics
    • T.M. Keesey: Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
    • S. Lewis: Functional Gene Ontology Annotation across Species using PAINT
    • S. McKay: GBrowse_syn
    • M. Porter: iBarcode-nextgen: tools for next generation biodiversity analysis
    • D. Rosauer: Biodiverse, a tool for spatial analysis of biological diversity
    • R. Scherle: The Dryad Digital Repository
    • C.L. Strope: indel-Seq-Gen version 2.0
    • M. Youngblood: mt-tRNA-Draw
  • Challenge demonstrations
    • M. Porter: GenGIS
    • K. Urie: VoLE (Viewer of Life in EOL)
    • V. Gopalan: Nexplorer3
    • A. Hill: PhyloBox
    • S. Smits: jsPhyloSVG
Summary of Day 1. 

Here are some tweets summarizing Day 1:
At the end of the day, I had dinner with Steven Kembel and Tom Sharpton (@toronaga) who I work with on a Gordon and Betty Moore Foundation funded project we call iSEEM.  Dinner and conversation were great.  I then went for a walk along the river and went back to my room.

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