Category: Misc.

UC Davis Summer Bioinformatics Workshops — Registration is Open!

Registration is open for the 2014 Bioinformatics Summer Workshops!

Now in it’s 7th year, the UC Davis Bioinformatics Training Program will be holding two week-long workshops this summer:

June 16-20, 2014: Using Galaxy for Analysis of High Throughput Sequence Data

Sept. 15-19, 2014: Using Command Line for Analysis of High Throughput Sequence Data

These workshops will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated.

Details

Both workshops will cover modern high throughput sequencing
technologies, applications, and ancillary topics, including:

· Illumina HiSeq / MiSeq, and PacBio RS technologies

· Read Quality Assessment & Improvement

· Genome assembly

· SNP and indel discovery

· RNA-Seq differential expression analysis

· Experimental design

· Hardware and software considerations

· Cloud Computing

Each workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data.

In June, workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the Amazon Cloud
(http://aws.amazon.com/) which allows for powerful web-based data analyses. There are no prerequisites other than basic familiarity with genomic concepts.

In September, exercises will be performed using the Linux command line. Therefore, for this workshop, it is strongly recommended that participants should also have basic familiarity with the Linux/Unix (or Mac) command line.

Who Should Attend

Prior course participants have included faculty, post docs, grad students, staff, and industry researchers. Anyone with an interest in sequence analysis is welcome!

Registration Info

Attendance is limited to 35 participants per workshop in order to foster an effective learning environment and ensure sufficient one-on-one attention. Course tuition is $1,500 for academic or non-profit participants and $1,800 for other participants. Amazon has kindly provided grants of $100 per participant for Amazon Web Services accounts. This will allow you to perform analysis during and after the course using Amazon’s resources, without purchasing your own high performance computing servers!

To register, click on the links above or go to
training.bioinformatics.ucdavis.edu/. We now accept credit cards, as well as UC recharge accounts, for payment. Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Questions

If you have any questions, please don’t hesitate to contact us:

· Core main telephone line: 530-752-2698

· Core email: bioinformatics.core@ucdavis.edu

See you this summer!

The UC Davis Bioinformatics Core Team

http://training.bioinformatics.ucdavis.edu

http://bioinformatics.ucdavis.edu/

Alana Firl talk today at #UCDavis 1:30 PM – From retinas to roots

Today there will be a talk by Alana Firl, one of the candidates for the new UC Davis “New Biology” post doctoral position –
http://biosci.ucdavis.edu/ecards/articles/bridging-fellowships.html.

Her talk will be on “Development of functional neural circuits in the retina” at 1:30 PM in LS1022.

In addition, and in a bit of a switch, she is proposing to do her post doctoral work on plant – microbe interactions (with myself and Sundar http://www-plb.ucdavis.edu/Labs/sundar/).  She will be discussing that proposed work briefly as well.

Postdoc Position in Innovating Communication in Scholarship

3/17/2014

Postdoc Position in Innovating Communication in Scholarship

A new UC Davis initiative on “Innovating the Communication in Scholarship” (http://icis.ucdavis.edu/) is hiring a 2 year postdoctoral fellow, starting July 1, 2014. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of academic misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, participate in pedagogical activities, and assist in grant writing. A Ph.D. or equivalent degree is required in Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or Literature. Other disciplines will be considered depending on the specific focus of the candidate’s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
We encourage applicants from historically under-represented groups, as well as individuals who can contribute to the diversity and excellence of the academic community through their research, teaching, and/or service.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli (mbiagioli@ucdavis.edu), MacKenzie Smith (macsmith@ucdavis.edu), Jonathan Eisen (jaeisen@ucdavis.edu).
Applications are due by April 15, 2014.
——–
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.

——–

Abstract Submission now open: Automated Function Prediction

(Please repost as appropriate; apologies for cross-posting and duplications).

An ISMB Special Interest Group Meeting: Automated Protein Function Prediction

Keynote speakers: Philip Bourne, National Institutes of Health, USA; Fiona Brinkman, Simon Fraser University, Canada; Mark Gerstein, Yale University, USA

Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, while the fraction of genes whose function is known is decreasing. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry.

The AFP SIG has been part of ISMB since 2005. We call upon all researchers involved in gene and protein function prediction to submit an abstract to the AFP meeting. Authors of select abstracts will be invited to give a talk and/or present a poster.

This year’s AFP meeting will also feature talks by creators of the best performing methods in the second Critical Assessment of Function Annotations or CAFA2 challenge.

Key dates:

April 18, 2014: Deadline for submitting abstracts.

May 9, 2014: Notifications for accepted abstracts e-mailed to corresponding authors

May 16, 2014: Deadline for presenters to confirm acceptance of invitation to speak.

July 11-12, 2014: AFP SIG preceding ISMB 2014

More information and to submit: http://biofunctionprediction.org/

Collecting my posts from various blogs, all in one place …

Trying to just compile my posts from various blogs I contribute to all in one place so decided to do it here.  These are posts for the last month or so

From the Innovating Communication in Scholarship blog and Website

Posts of mine at the microBEnet blog

UC Davis ADVANCE
——–
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.

——–

#UCDavis College of Biological Sciences New Biology PostDoc Candidates Talks

Cool science education kickstarter of the month: a hundred tiny hands

This looks very cool. And important. 100 tiny hands Kickstarter campaign.

https://www.kickstarter.com/projects/2084593011/a-hundred-tiny-hands-toys-for-your-brilliant-lil-i/widget/video.html

——–
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.

——–

Dean Robert Post 3/14/14 The Constitutional Dimensions of Academic Freedom

Posting this announcement I got:

Dear UC Davis Faculty, Staff, Students and Community Members,

We would like to remind you that the next event in the Provost’s Forums on the Public University and the Social Good, which is co-sponsored with the  Academic Senate’s Committee on Academic Freedom and responsibility, will be held on Friday, March 14, 2014.

Robert Post, Dean and Sol & Lillian Goldman Professor of Yale Law
School will speak on the topic of “The Constitutional Dimensions of
Academic Freedom”.  After his talk, he will be joined by a panel
comprised of Ralph Hexter, Provost and Executive Vice Chancellor at UC
Davis, Roberta Rehm, Associate Professor in the Department of Family
Health Care Nursing at UC San Francisco, and Henry Reichman, Professor
Emeritus of History at CSU Easy Bay and First Vice President of the
AAUP and its Committee A on Academic Freedom and Tenure.Prior to assuming his position as Dean of the Yale Law School, Dean
Post spent twenty years as a professor at the UC Berkeley School of

Law. His areas of expertise include constitutional law, First
Amendment law, legal history, and equal protection. He has written and
edited numerous books, including, For the Common Good: Principles of
American Academic Freedom (2009), and more recently Democracy,
Expertise, Academic Freedom: A First Amendment Jurisprudence for the
Modern State (2012).The event will begin at 2 p.m. in the Vanderhoef  Studio Theatre at
the UC Davis RobertMondavi Center. It is free and open to the general public. There will
be a reception with light refreshments directly following the lecture
in the Yoche Dehe Grand Lobby of the Mondavi Center.

If you are unable to attend this event, videos of all Provost’s Forums
lectures are available to the public and can be found on the official
Provost’s Forums website

(http://provost.ucdavis.edu/initiatives-and-activities/activities/future/past-events.html).

Our most recent lecture, “The Public University: What Should We Be
Doing on Climate Change?”  featuring Professor Naomi Oreskes, is now
available for viewing along with all of the 2013-2014 season lectures.For more details and information on this event, please see the
attached flyer, visit our website: The Provost’s Forum on the Public
University and the Social Good (http://provost.ucdavis.edu/initiatives-and-activities/activities/future/index.html), or contact Casey Castaldi (cvcastaldi@ucdavis.edu).

In addition, please forward this information to any interested parties, as all events are open to the public. We hope to see you at this important event!

Robert Post 3.14 Flyer.pdf

A must read: How to Level the Playing Field for Women in Science by Mary Ann Mason

This is a must read for anyone interested in Science / Academia: How to Level the Playing Field for Women in Science – Advice – The Chronicle of Higher Education.  By Mary Ann Mason, who is a professor at UC Berkeley and has extensive experience on studying issues relating to women in science and academia.  She details in this article four key things that can be done to reduce the “baby penalty”:

  • Better (and more) child-care options
  • Effective dual-career policies
  • Childbirth accommodations
  • Compliance with Title IX 
Definitely worth reading.  And worth checking out some of the web material from her including
(Thanks to Madhu Katti – who posted this to Facebook)
——–
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.

——–

Another Mostly Male Meeting from UCSD- should be called "Food and Fuel for the 19th Century"

Well, just when I thought meeting organizers from UCSD had learned their lesson regarding mostly male meetings – this comes along.  Check out “Food and Fuel for the 21st Century” (I was pointed to this by a comment on a blog post of mine). The speakers are

That a ratio of 18:2 or 10% female.  
Not that I know the cause of this but here are some other pieces of information to consider.
The Food and Fuel for the 21st Century Program lists 5 people on their Executive Committee.  Any guesses on the # of these that are men?  Well it is 5.
Fortunately they have an Advisory Committee too and that must have some women on it right?  Nope.

Reminds me a bit of the QBio meeting from 2013 organized by many from UCSD which I wrote about last year: Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome because they don’t take a XX.  I note – this years Q-Bio meeting is much better.  But one can ask – does nobody at UCSD think about these issues when planning conferences and Advisory / Executive Committees.  I personally don’t think one should choose women to just choose women.  But as with the Q-Bio meeting from last year, I think there are an enormous number of highly qualified women working on topics directly related to “Food and Fuel for the 21st Century” and thus I am both surprised and disturbed by the gender ratio of this meeting and this organization.

UPDATE 3/4 7:21 AM

It took me a bit but I found details on the 2013 symposium from the same group.  The web site for the 2013 meeting is not active as far as I can tell.  However it is available in the Internet Archive.  For example, here is a snapshot from June 1, 2013.  From that snapshot here are the listed speakers

  • David Kramer, Michigan State University
  • Susan Golden, University of California, San Diego
  • Julian Schroeder, University of California, San Diego
  • Stephen Mayfield, University of California, San Diego
  • Steven Briggs, University of California, San Diego
  • Matteo Pellegrini, University of California, Los Angeles
  • Donald Weeks, University of Nebraska–Lincoln
  • Michael Burkart, University of California, San Diego
  • Chancellor Pradeep Khosla, University of California, San Diego
  • Farzad Haerizadeh, Life Technologies
  • Ben Hueso, California State Assembly
  • Bill Gerwick, Scripps Institution of Oceanography
  • Eric Mathur, SG Biofuels
  • James Van Etten, University of Nebraska–Lincoln
  • Fred Tennant, Heliae
  • David Dunigan, University of Nebraska–Lincoln
  • Xuemei Bai, Cellana
  • George Oyler, University of Nebraska–Lincoln
  • Gerry Mackie, University of California, San Diego
  • Mark Hildebrand, Scripps Institution of Oceanography
  • Lawrence Johnson, Salim Group
  • Craig Behnke, Sapphire Energy
  • Rebecca White, Sapphire Energy

For a ratio of 20:3.

——–
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.

——–