Tag: meetings

Come all ye Citizen Microbiologists – to Denver 5/19 for ASM Meeting – abstracts due 1/15

This is going to rock.  Citizen microbiology – highlighted at the American Society for Microbiology Annual Meeting in Denver in May.  The details on the session are below.  Sunday May 19 at the American Society for Microbiology General Meeting in Denver.  If you are interested in attending Register here.  If you work on some aspect of Citizen Microbiology please consider submitting an abstract for a talk or poster. The deadline is January 15.  We will highlight ALL accepted abstracts in some way both during the session and in blogs, tweets, interviews, etc.  So please consider participating.
Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public OralAbstract Image
3:00 p.m.- 5:30 p.m.
Conveners:
JONATHAN EISEN; Univ. of California-Davis, Davis, CA
DAVID COIL; Univ. of California-Davis, Davis, CA
Invited Speakers:
GRAHAM HATFULL; Univ. of Pittsburgh, Pittsburgh, PA
   Carski Foundation Distinguished Undergraduate Teaching Award and Division W Lecturer
DARLENE CAVALIER; Sci. Starter, Sci. Cheerleader, Philadelphia, PA
ROB DUNN; North Carolina State Univ., Raleigh, NC
Description:
Citizen Science is a valuable way to both generate scientific data and to engage and educate a broad audience. Some areas of biology such as astronomy and ornithology have conducted multiple successful citizen science projects over the years. Surprisingly, there are not many citizen science projects in microbiology even though microbes are of interest to the majority of the public, as well as being tractable for these kinds of studies. This session will focus on citizen science in microbiology. This session will examine the diversity of Citizen Science projects, outline what makes a successful project, and highlight examples of past, current and future Citizen Microbiology projects. Speakers will also provide details on overcoming challenges in Citizen Science (e.g., visualization, permissions, privacy, standardization, informed consent). Our belief is that more projects, throughout the different domains of microbiology, could benefit from incorporating a citizen science component. Having this session at the General Meeting will help bring together people interested in this topic, as well as fostering collaboration on existing and future citizen science projects.
Sunday May 19 at the American Society for Microbiology General Meeting in Denver.  Register here.

——–
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.

——–

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

http://storify.com/phylogenomics/lake-arrowhead-microbial-genomes-2012-lamg12.js?template=slideshow[View the story “Lake Arrowhead Microbial Genomes 2012 #LAMG12” on Storify]

——–
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.

——–

Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don’t take a XX

Wow.  Just wow.  And not in a good way.  Just got an email invitation to a meeting.  The meeting is

“THE FIRST ANNUAL WINTER Q-BIO MEETING: Quantitative Biology on the Hawaiian Islands. February 18-21, 2013.”  

Well, I mean – who wouldn’t want to go to Hawaii for a meeting.  And a meeting that 

“brings together scientists and engineers who are interested in all areas of q-bio.”  

Plus 

“Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio.”

So I could go to Hawaii each year.  Cool.  And 

“The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.”  

I like synthetic biology and, well, sometimes I like experts, so still good

But then, OMG, then, the confirmed speaker list and the conference organizers.

2013 CONFIRMED SPEAKERS:

  1. Jim Collins, Boston University
  2. Johan Elf, Uppsala University
  3. Michael Elowitz, California Institute of Technology
  4. Timothy Elston, UNC Chapel Hill School of Medicine
  5. James E. Ferrell, Stanford University 
  6. Martin Fussenegger, ETH Zurich
  7. Leon Glass, McGill University
  8. Terry Hwa, University of California, San Diego
  9. Roy Kishony, Harvard Medical School
  10. Galit Lahav, Harvard University
  11. Andre Levchenko, Johns Hopkins University
  12. Wendell Lim, University of California, San Francisco
  13. Andy Oates, The Max Planck Institute, Dresden
  14. Bernhard Palsson, University of California, San Diego
  15. Gurol Suel, UT Southwestern Medical Center
  16. Chao Tang, Peking University
  17. John Tyson, Virginia Tech
  18. Craig Venter, The J. Craig Venter Institute
  19. Chris Voigt, Massachusetts Institute of Technology
  20. Ned S. Wingreen, Princeton University  

CONFERENCE ORGANIZERS:

  1. Bill Ditto, University of Hawaii 
  2. Jeff Hasty, UC San Diego 
  3. Bill Hlavacek, University of New Mexico
  4. Alex Hoffmann, UC San Diego
  5. Brian Munsky, New Mexico Consortium 
  6. Lev Tsimring, UC San Diego 
That is a 25:1 ratio.  Pathetic.  Embarrassing.  The sponsors – UC San Diego’s Division of Biological Sciences and BioCircuits Institute, San Diego Center for Systems Biology, the University of Hawaii and the Office of Naval Research – should all be ashamed.

For other posts on this topic see

UPDATE – I have now submitted an abstract to the meeting.  The abstract I submitted is available here and posted below

The probability of having one out of twenty six participants at a scientific meeting be female

A quantitative analysis of gender bias in quantitative biology meetings 
Jonathan A. Eisen
University of California, Davis
(Note – new title suggested by John Hogenesch)
Scientific conferences have key participants which I define to be the speakers and the organizers. Such key participants can be divided into two main classes based on gender: male and female, which I denote here as M and F, respectively (I realize there are other gender classes and I regretfully am not including them here). The number of key participants (which I denote as KP) for conferences varies significantly. For this analysis I focused on meetings with KP = 26. This value was selected for multiple reasons, including (a) that it is the number of letters in the English alphabet (b) that its factors include the number 13 which I like, and (3) because in email announcements for this meeting KP= 26. I sought to answer a relatively simple question – what is the probability that, for a meeting with KP=26, that F = 1. I chose this because this seemed extreme and because F=1 in the email announcements for this meeting. Using the probability mass distribution formula as below:
which becomes

n = NP = number of participants
k = f = the number that are female
p = percentage of f in population being sampled

I have calculated Pr (F=1) for KP = 26. Assuming for the moment that p = 0.5 (i.e., that the population to be sampled is 50:50 male vs female) then Pr (F=1) = 3.8743E-07. This is highly unlikely by chance alone. However the assumption of p = 0.5 is certainly off in some fields. I therefore calculated P (F=1) for different frequencies of F in the population (i.e., what is the expected ratio of females to sample from).

Thus for a meeting with NP = 26, only when the frequency of F is ~0.16 does P (F=1) exceed 0.05. So a question is then, what should we use for p for this meeting? An informal survey (John Hogenesch, posted to Facebook at https://www.facebook.com/jonathaneisen/posts/10151208978630767?comment_id=24634832&offset=0&total_comments=15 ) suggests that in qBio the percentage is about 20%. However that may not be an ideal estimate since this meeting is specifically about synthetic biology, I do not have a any estimate of p for this field. However, examination of key meetings in the field (e.g., see http://syntheticbiology.org/Conferences.html for a list) reveals a percentage of perhaps a bit higher. For example at SB5 the ratio was about 35%. I conclude that it is likely that p > 20% in Synthetic Biology. Given that for p = 0.2 the Pr (F=1) < 0.05 I therefore conclude that the null hypothesis (that having one female out of 26 key participants) can be rejected – and that this meeting has a biased ratio of males: females.

UPDATE 2: Here is the full email I received, just for the record

ABSTRACT SUBMISSION DEADLINE 09/15/12http://w-qbio.org/abstracts.html

THE FIRST ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 18-21, 2013http://w-qbio.org/

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio. The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.

SPONSORED BY:UC San Diego’s Division of Biological Sciences and BioCircuits Institute
San Diego Center for Systems Biology
University of Hawaii
Office of Naval Research

2013 CONFIRMED SPEAKERS:
Jim Collins, Boston University
Johan Elf, Uppsala University
Michael Elowitz, California Institute of Technology
Timothy Elston, UNC Chapel Hill School of Medicine
James E. Ferrell, Stanford University
Martin Fussenegger, ETH Zurich
Leon Glass, McGill University
Terry Hwa, University of California, San Diego
Roy Kishony, Harvard Medical School
Galit Lahav, Harvard University
Andre Levchenko, Johns Hopkins University
Wendell Lim, University of California, San Francisco
Andy Oates, The Max Planck Institute, Dresden
Bernhard Palsson, University of California, San Diego
Gurol Suel, UT Southwestern Medical Center
Chao Tang, Peking University
John Tyson, Virginia Tech
Craig Venter, The J. Craig Venter Institute
Chris Voigt, Massachusetts Institute of Technology
Ned S. Wingreen, Princeton University

CONFERENCE ORGANIZERS:
Bill Ditto, University of Hawaii
Jeff Hasty, UC San Diego
Bill Hlavacek, University of New Mexico
Alex Hoffmann, UC San Diego
Brian Munsky, New Mexico Consortium
Lev Tsimring, UC San Diego

***REGISTRATION NOW OPEN***
Registration fee covers conference venue, opening reception, banquet, coffee & snacks.

EARLY BIRD ($450.00) REGISTRATION DEADLINE: December 1, 2012
REGULAR REGISTRATION ($550) DEADLINE: February 5, 2013

REGISTER NOW: http://w-qbio.org/abstracts.html

HOTEL: A block of rooms have been reserved for registered conference participants available for a negotiated rate of $199 per night at the Hilton Hawaiian Village in Waikiki. The rooms are available on first come first serve basis and will be available soon, so book early!

CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the September 15th deadline. Abstract guidelines and submission information at:http://w-qbio.org/guidelines.pdf

ABSTRACT DEADLINE: September 15, 2012
Accepted abstracts will be announced October 31, 2012.

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

Questions should be emailed to: coordinator@w-qbio.org

UPDATE 4:  (9/18/12)

Plus some links that may be of relevance

UPDATE 6: 9/23/12

Some more links on the recent PNAS paper on gender bias and evaluating scientists

UPDATE 7:  9/23/12

Interesting article on gender and invitations to write major reviews
UPDATE 8: More follow up to the Gender Bias study from PNAS 9/26

UPDATE 9: Other posts on gender bias of interest

UPDATE 10: 11/21/13

Just got this in my email.  Kudos to the people behind qBio for adding more women to their planning committee and adding a many women to the speaker list.
***ABSTRACT SUBMISSION DEADLINE EXTENDED TO MONDAY, DECEMBER 2, 2013***
http://w-qbio.org/abstracts/

UPDATE:  In response to participant interest, the submission deadline has been extended to December 2, 2013.  This year 15 contributed talks will be selected from the submitted abstracts to be presented with the invited talks during the plenary sessions.  Contributed talks will also be selected for parallel breakout sessions which commence in the late afternoon.

THE SECOND ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 17-20, 2014
http://w-qbio.org/

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. The venue for 2014 is the Hilton Waikoloa Village, which is located on the Kohala Coast of Hawaii’s Big Island. The resort lets you experience breathtaking tropical gardens, abundant wildlife, award-winning dining, world-class shopping, art and culture, and an array of activities. The Island of Hawaii is the youngest and biggest in the Hawaiian chain, providing a vast canvas of environments to discover–home of one of the world’s most active volcanoes (Kilauea), the most massive mountain in the world (Maunaloa), and the largest park in the state (Hawaii Volcanoes National Park).

SPONSORED BY:
UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology
The University of Hawaii at Manoa
UC San Diego Divisions of Biological Sciences and Engineering
The Office of Naval Research

2014 CONFIRMED SPEAKERS:
Naama Barkai, The Weizmann Institute of Science
Sangeeta Bhatia Massachusetts Institute of Technology
Hana El-Samad, University of California, San Francisco
Zev Gartner, University of California, San Francisco
Taekjip Ha, University of Illinois
Shigeru Kondo, Osaka University
Arthur Lander, University of California, Irvine
Andrew Murray, Harvard University
Steve Quake, Stanford University
Petra Schwille, Max Planck Institute
Christina Smolke, Stanford University
Aleksandra Walczak, Laboratoire de Physique Théorique

CONFERENCE ORGANIZERS:
Kevin Bennett, University of Hawaii at Manoa
William Ditto, University of Hawaii at Manoa
Hana El-Samad, University of California, San Francisco
Jeff Hasty, University of California, San Diego
Alexander Hoffmann, University of California, San Diego
Galit Lahav, Harvard University
Eva-Maria Schoetz-Collins, University of California, San Diego
Chao Tang, Peking University
Lev Tsimring, University of California, San Diego

***REGISTRATION NOW OPEN***
Registration fee covers conference venue, registration reception, banquet, coffee & snacks.

EARLY BIRD REGISTRATION ($500/$425 Student) DEADLINE: December 20, 2013
REGULAR REGISTRATION ($600/$525 Student) DEADLINE: January 31, 2014
LATE REGISTRATION ($675/$600 Student) After January 31, 2014

REGISTER NOW: http://w-qbio.org/

HOTEL:  A block of rooms has been reserved for registered conference participants at a negotiated rate of $199 per night at the Hilton Waikoloa Village. The rooms will be available soon on a first-come, first-served basis, so book early!

CONTRIBUTED TALKS:  If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 5th deadline. Abstract guidelines and submission information at: http://w-qbio.org/abstracts/

ABSTRACT DEADLINE: EXTENDED UNTIL MONDAY, December 2, 2013 (Extended due to large volume of interest!)
Accepted abstracts will be announced by December 6, 2012.  You may submit your abstract now and if accepted, still register by the early bird registration deadline of December 20, 2013.
Abstract guidelines and submission information at: http://w-qbio.org/abstracts/

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

Questions should be emailed to: coordinator@w-qbio.org

——–
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.

——–

Slides and slideshow w/ audio from my talk at Bay Area Illumina User’s Meeting

Just quick post … gave a talk Thursday at the Bay Area Illumina User’s meeting.  I have posted my slides to Slideshare and a Video Slideshow with audio to Youtube.

——–
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.

——–

"Genomics: the Power and the Promise" meeting – could be called "Men Studying Genomics" instead

Just got another email advertising this meeting: Genomics: the Power and the Promise.  Organized by Genome Canada and the Gairdner Foundation.  And, well, though I love some of the things Genome Canada has done, this conference really stick in my craw in the wrong way. Why?  It has a serious male speaker overabundance.  Here is the list of speakers:

Day 1 

  1. Pierre Muelien
  2. John Dirks
  3. Gary Goodyear
  4. Eric Lander
  5. Craig Venter
  6. Philip Sharp
  7. Svante Paabo
  8. Tom Hudson
  9. Peter Jones
  10. Stephen Scherer
  11. Michael Hayden
  12. Bertha Maria Knoppers

Day 2

  1. Stephen Mayfield
  2. Elizabeth Edwards
  3. Curtis Suttle
  4. Peter Langridge
  5. Michel Georges
  6. William Davidson
  7. Klaus Ammann

That is 17:2 male: female ratio. That is one female speaker per day.  Not impressive.

On Day 2 there are two panels (which generally I do not count as “speakers” but at least there are a few more women on these):

  • Panel 1: Sally Aitken, Vincent Martin, Elizabeth Edwards, Curtis Suttle, Gerrit Voordouw, Steve Yearley
  • Panel 2: William Davidson, Martine Dubuc, Isobel Parkin, Graham Plastow, Curtis Pozniak, Peter Phillips 

So if you count these that then comes to a ratio of presenters of 25: 6.  Do I want quotes for meetings?  No, but given that the ratio of men: women in biology is close to 1:1 this suggests to me some sort of bias.  Where does this bias come from?  I don’t know.  Could be at the level of who gets invited.  Could be at the level of who accepts.  Could be some non obvious criterion for selecting speakers that leads to a bias towards men.  I don’t know.  But I personally think they could do better.  And I note – they could probably do better in terms of other aspects of diversity of speakers, but I am focusing here just on the male vs. female ratio.  Again, I am not suggesting one should have quotas for all meetings but at the same time, a 17:2 male to female speaker ratio suggests something could use some working on.

As a side story I decided to look at some past conferences sponsored by Genome Canada.  I worked my way down the list … see below:

  • 2008 Joint IUFRO-CTIA International conference. Speakers: 8:2 male: female
  • 6th Canadian Plant Genomics Workshop Plenary Speakers 8:2
  • 8th Annual International Conference of the Canadian Proteomics Initiative.  See below.  32:2 male to female.  I have no idea what the ratio is in the field of proteomics but this is a very big skew in the ratio.  94% male.  
    1. Leigh Anderson (Plasma Proteome Institute)
    2. Ron Beavis (UBC)
    3. John Bergeron (McGill)
    4. Christoph Borchers (UVic)
    5. Jens Coorssen (U Calgary)
    6. Al Edwards (U Toronto)
    7. Andrew Emili (U Toronto)
    8. Leonard Foster (UBC)
    9. Jack Greenblatt (U Toronto)
    10. Juergen Kast (UBC)
    11. Gilles Lajoie (U Western Ontario)
    12. Liang Li (U Alberta)
    13. John Marshall (Ryerson)
    14. Susan Murch (UBC Okanagan)
    15. Richard Oleschuk (Queens)
    16. Dev Pinto (NRC)
    17. Guy Poirier (Laval)
    18. Don Riddle (UBC)
    19. David Schreimer (University of Calgary)
    20. Christoph Sensen (University of Calgary)
    21. Michael Siu (York)
    22. John Wilkins (University of Manitoba)
    23. David Wishart (University of Alberta)
    24. Rober McMaster (Universiyt of British Columbia)
    25. Peter Liu (University of Toronto)
    26. Christopher Overall (Universiyt of British Columbia)
    27. John Kelly (NRC, Ottawa)
    28. Joshua N. Adkins (Pacific Northwest National Laboratory, USA)
    29. Dustin N.D. Lippert (University of British Columbia)
    30. David Juncker (McGill University)
    31. Jenya Petrotchenko (University of Victoria)
    32. Detlev Suckau (Bruker Daltonik GmbH)
    33. Peipei Ping (University of California)
    34. Robert McMaster (University of British Columbia)
I couldn’t bear to go on any further.
Now – note – I am not accusing anyone of bias here.  But I do think it might be a good idea for Genome Canada to put some more effort into figuring out why the conferences they sponsor have such skewed ratios.  And perhaps they can try to do something about this.  For more on this issue from my blog see
——–
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.

——–

History of the Lake Arrowhead Microbial Genomes meetings

Recommended meeting for those interested in microbial diversity and/or microbial genomics: Microbial Genomics – ARROWHEAD 2012

Among the reasons to go:

And if you want to know more about past meetings see below:

——–
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.

——–

Holy s$&# – I am going back to #SciFoo

Well, I cannot wait until Friday.  I am going back to SciFoo.  Best.  Meeting.  Ever.  Went in 2006 & 2007.  Changed my life.  Here are some posts – back when I was a very newbie blogger:

2006

2007
——–
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.

——–

Three talks, 1.5 days at #ISMB … phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the “Intelligent Systems for Molecular Biology” (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these “slideshows” to YouTube. Here are the talks below:

Talk 1 for the “Bioinformatics Open Source Conference” BOSC2012.  Was asked to talk about Open Science … so … I did …

Slides: Jonathan Eisen talk on “Open Science” at #BOSC2012 #ISMB

View more presentations from Jonathan Eisen

Slideshow with audio:
 

Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of “lessons learned” …


Slides:Jonathan Eisen talk for #SCS2012 at #ISMB “Networks in genomics and bioinformatics: from phylogeny to Twitter”

View more presentations from Jonathan Eisen

Slideshow with audio:

Talk 3 for the “Automated function prediction” AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction …

Slides:Jonathan Eisen talk “Phylogneomic approaches to functional prediction”a #AFP2012 #ISMB

View more presentations from Jonathan Eisen

Slideshow with audio:

http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings.js[&amp;lt;a href=”http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings&#8221; target=”_blank”&amp;gt;View the story “Jonathan Eisen @phylogenomics talks at #ISMB Satellite Meetings” on Storify&amp;lt;/a&amp;gt;]

——–
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.

——–

Pics from the Redrum hotel in DC where we stayed for #SAMG12

Img_3376 Img_3369

Img_3357

See the full gallery on Posterous

IMG_3368.MOV Watch on Posterous

IMG_3362.MOV Watch on Posterous

IMG_3370.MOV Watch on Posterous

IMG_3377.MOV Watch on Posterous

IMG_3371.MOV Watch on Posterous
——–
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.

——–

At IOM Forum on Microbial Threats "Science And Applications of Microbial Genomics" #SAMG12

At IOM Forum on Microbial Threats “Science And Applications of Microbial Genomics” meeting in DC. To find out current details on the meeting check out Twitter hashtag #SAMG12. See feed below (though it is easier to go to Twitter to follow #SAMG12).
http://widgets.twimg.com/j/2/widget.jsnew TWTR.Widget({ version: 2, type: ‘search’, search: ‘#SAMG12’, interval: 30000, title: ‘IOM Meeting on “Science and Applications of Microbial Genomics”‘, subject: ‘All microbes, all the time’, width: 500, height: 1000, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: false, loop: false, live: true, behavior: ‘all’ } }).render().start();

——–
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.

——–