Tag: informatics

Discussion of new pathogen discovery papers

Interesting discussion yesterday with authors of new pathogen discovery papers. I will try to write more about this later but am heading out the door so this Storify will have to do for now.

//storify.com/phylogenomics/discussion-of-pathogen-discovery-papers/embed?border=false//storify.com/phylogenomics/discussion-of-pathogen-discovery-papers.js?border=false[View the story “Discussion of pathogen discovery papers” on Storify]
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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iEVOBIO Call for Lightning Talks #Evolution #InOklahoma

Just got this email and thought I would repost:

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The Call for Lightning Talks is now open for the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), athttp://ievobio.org/ocs/index.php/ievobio/2011. See below for instructions.

Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information ( http://ievobio.org/faq.html#lightning). Lightning talks will be part of the more interactive afternoon program on both conference days.

Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization.


Submissions consist of a title and an abstract at most 1 page long.  The abstract should provide an overview of the talk’s subject.  Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met.

Review and acceptance of lightning talks will be on a rolling basis.  The deadline for submission is the morning of the first day of the conference (June 21). Note that the number of lightning talk slots is finite, and given the high volume of submissions we experienced for full talks, the Lightning Talks track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time.

We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above.

Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see  http://ievobio.org/challenge.html), and information on the Software Bazaar and Birds-of-a-Feather sessions is forthcoming.

More details about the program and guidelines for contributing content are available at  http://ievobio.org.  You can also find continuous updates on the conference’s Twitter feed athttp://twitter.com/iEvoBio.

iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL).

The iEvoBio 2011 Organizing Committee:
Rob Guralnick (University of Colorado at Boulder) (co-Chair)
Cynthia Parr (Encyclopedia of Life) (co-Chair)
Dawn Field (UK National Environmental Research Center)
Mark Holder (University of Kansas)
Hilmar Lapp (NESCent)
Rod Page (University of Glasgow)

(*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see  http://www.opensource.org/docs/definition.php) and 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 a recognized Open Source License (see http://www.opensource.org/licenses/), 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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Summary of #iEVOBIO Day 2, #phylogenetics #informatics #opensource #biodiversity #evolution

This is a continuation of notes on iEVOBIO meeting.  Much of this comes from twitter.  Additional comments will be posted over the next few days.  See notes on Day 1 here. Note – thanks to the people who answered my query on twitter about how to remove spurious html code from pages – I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html.  I ended up using Zubrag which was suggested by brendanwlocke.

Day 2. Beginning.

Since I was leaving that PM I could not borrow a hotel bike and bike over again.  So I walked from the hotel, along the river 2 or so miles, after getting coffee.  I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seemed very good.  But I find if I do not get some exercise every day at a meeting I go crazy so it was worth it.  Here are some notes on Day 2.

Day 2. Part 1. Keynote

Alas, I missed much of the keynote.  But what I caught was good.  Here are some notes, mostly from twitter. And also see Rob G’s slides below

RPG iEvoBio 2010 Keynotehttp://static.slidesharecdn.com/swf/ssplayer2.swf?doc=ievobiokeynote3-100630154451-phpapp02&stripped_title=rpg-ievobio-2010-keynote

Rob Guralnick: Biodiversity Discovery and Documentation in the Information and Attention Age

    Day 2. Part 2. Short talks.

    Day 2. Part 3. Lunch

    Went to lunch with a small group to the People’s Sandwich of Portland.  Took the light rail over the river.  Portland has some really nice features – like free light rail in the city.

    Day 2. Part 4. Lightning Talks

    Day 2. Part 5. Birds of a feather


    Then there were breakout sessions which were called “Birds of a feather”  I went to one discussing open access and fair use issues. 

    Day 2. Part 6. Wrap up and other general information

    And then I had to go home.  The meeting wrapped up as I was leaving. Here are some ending tweets:

    Some other general info tweets:

    Post meeting posts and blogs
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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.

    Jonathan Eisen talk at #ievobio 2010http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-100629132410-phpapp01&stripped_title=eisen

    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:

    • oatp Open science and data sharing at Evolution 2010 andiEvoBio: Posted by petersuber to oa.notes oa.biology oa.new oa… http://bit.ly/bOocHh
    • chrisfreeland @rdmpage @cydparr sounds like #ievobio is going well & interesting. v. sorry I couldn’t work it in!
    • trinaeroberts Demos of Biodiverse, GenGIS, various tree visualizers… very cool stuff at #iEvoBio today!
    • justsayinnn someone explain to me how the ievobio wants open source yet they charged for registration???
    • justsayinnn data visualization stuff was way cool today at #ievobio

    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.

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–