Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Simple microbiome quiz and then mapping function from PGED

Just did this: Map-Ed Genetics: Pin Yourself on Our World Map! (the microbiome one – there are two right now – the other is personal genomics – and others coming).  Best part is browsing the map of other participants afterwards.

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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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mBio – home of some really cool, #openaccess microbiology papers

Am really enjoying the suite of papers coming out in mBio – the Open Access PLOSOne like journal from the American Society for Microbiology.  Here are some examples of recent papers that caught my eye:

And many many more.  Kudos to ASM and mBio.

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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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is Sexxing up your scientific journal OK? The Journal of Proteomics seems to think so

I saw a Tweet from a college classmate of mine –  Jillian Buriak – that pointed me to this article from the Journal of Proteomics in January 2012.

Harry Belafonte and the secret proteome of coconut milk

And this is what one sees when one goes there:

A “Graphical Abstract” with the text “Here is your coconut woman, as perhaps envisioned by Harry Belafonte. For its proteome, though, have a look at the report inside!”.  I guess this is an attempt at a joke about breasts and coconuts?  And how is it appropriate for a scientific paper?

Want to guess about the gender balance of the people who run the journal? Here are the pics from the web site of the main executive editors and officials

Thoughts out there?  Seems pretty inappropriate to me …

UPDATE 3/21 8 AM – Storifying Twitter comments

//storify.com/phylogenomics/journal-of-proteomics-offensive-sexist-graphic-abs/embed//storify.com/phylogenomics/journal-of-proteomics-offensive-sexist-graphic-abs.js[View the story “Journal of Proteomics offensive sexist graphic abstracts” on Storify]

UPDATE 3/21 9:26 AM Elsevier says they will take down image but haven’t yet.  Bonus – you can download a PPT slide of the brilliant image

UPDATE 3/21 9:34 AM

Some links of relevance

UPDATE 3/22 12:34 PM
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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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An important read on “Impact Factor Mania” from Arturo Casadevall & Ferric Fang

Really important article in mBio: Causes for the Persistence of Impact Factor Mania.

Full citation : Casadevall A, Fang FC. 2014. Causes for the persistence of impact factor mania. mBio 5(2):e00064-14. doi:10.1128/mBio.00064-14.

In the article the authors discuss what they call “Impact Factor Mania” and outline what they believe the causes of it are (hyper competition for funding and jobs, paucity of objective measures of the importance of scientific work, hyper specialization of science, benefits to selected journals, benefits to scientists, national endorsements and prestige by association).  They then discuss some of the problems with such mania including distortions in the scientific enterprise, inability to accurately predict impact, ignoring many important studies, limited correlation between IF and article citation, imperfection of citation rate, delay in communications, and creation of perverse incentives.  They discuss some of the existing proposals for reform including DORA and a boycott of high impact journals.  And finally they discuss what scientists can do including: reforming criteria for funding and promotion, use of diverse metrics, increase interdisciplinary interactions, encourage elite journals to become less elite, and a return to essential scientific values.

The article is a perfect follow up on our recent “Publish or Perish” meeting.

June R Workshop from Pat Schloss

From Pat Schloss/ the Mothur-announce mailing list

Hi mothur fans,
I’ll be hosting another Crashcourse in R Workshop for Microbial Ecologists this June. The workshop will run from June 23rd to 25th near the Detroit airport. The workshop is being filled on a first come, first served basis. The workshop is geared towards people with interests in microbial ecology that would like to learn R or to learn it better so you shouldn’t feel like this isn’t for you if you are a beginner. I assume no previous computer programming experience. The workshop is an even blend of lecture/discussion and hands on use of R with real data and typically uses mothur output files as a starting point. This is a new workshop that I am offering, so here is a rough outline of what the workshop schedule will look like (it is subject to some minor changes)…
Monday:

AM Introduction to R – operations, variable types
PM R basics – getting data in and out, packages

Tuesday:

AM Plotting: Core functions
PM Plotting: Lattice / RGL

Wednesday:

AM Programming in R – Functions, loops
PM Programming in R – Controlling flow

Each day there will be a lecture and discussion interspersed with hands-on activities and it will run from 9 to 5. If you would like to meet with me one-on-one to discuss your project, I can do that in the evening and during breaks. Please email me for more details. Thanks,
Pat Schloss

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.
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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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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
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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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