Eisen Lab Blog

Article by Amy Maxmen "Preserving Research" on ways to share unpublished manuscripts

There is a nice article by Amy Maxmen in The Scientist titled “Preserving Research” on ways to share unpublished manuscripts. It includes some discussion of pros and cons of various archives including arXiv, Figshare, ResearchGate and more. Definitely worth a look.  There are of course many many many ways to share your articles before and after you publish them.

For more about sharing PDFs/articles see my post: The Tree of Life: Ten simple ways to share PDFs of your papers.  And of course, don’t forget that just posting your paper somewhere does not mean that it will continue to be available to all.  Also – the license that you use when sharing your article affects how people can use and reshare it so pay attention to the fine print and use as broad a license as possible …

——–
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.

——–

RFA Announcement – International Cooperative Biodiversity Groups (ICBG)

Forwarding this from ASM

 

ASM Society

RFA Announcement – International Cooperative Biodiversity Groups

Dear Colleague:

 

The Department of Health and Human Services, National Institutes of Health (NIH) and National Science Foundation (NSF) have requested that ASM bring to the attention of interested members the following RFA:

 

Limited Competition: International Cooperative Biodiversity Groups (U19)

 

Application Due Date(s): November 20, 2013, by 5:00 PM local time of applicant organization.

 

URL:  http://grants.nih.gov/grants/guide/rfa-files/RFA-TW-13-001.html

 

Synopsis: The National Institutes of Health and the National Science Foundation invite applications for the establishment or continuation of “International Cooperative Biodiversity Groups” (ICBG).  The program is built on the observation that natural products derived from organisms in nature remain the most productive source of new therapeutics, yet the biodiversity on which discovery of these drugs depends is rapidly disappearing around the world.  Consequently, the ICBG program supports international, public-private, interdisciplinary research teams in the exploration and discovery of novel compounds and extracts with potential for development as therapeutic agents for multiple disease targets, at the same time as it builds research capacity in partnering countries to support sustainable exploration and use of biodiversity and the knowledge to conserve it.  These goals are advanced through fair and equitable partnership frameworks among research organizations in the U.S. and in low and middle income countries (LMICs).

 

This competition of the International Cooperative Biodiversity Groups (ICBG) program continues several new emphases that began with the previous FOA, RFA-TW-08-010, including an emphasis on microbial and marine organisms, greater involvement of funded consortia with government contract resources, and greater use of molecular and genomic tools. This FOA also introduces some new features, including some new target health areas (neurological disorders and stroke, pain and inflammatory processes, and others, see Interests of NIH institutes and Centers, below) and an emphasis on supporting the scientific basis for integrated conservation and development efforts through research and research training rather than through direct implementation activities.

 

Award Information:

 

Funds Available and Anticipated Number of Awards: Issuing agencies and partner components intend to commit an estimated total of $3.3 mil for Fiscal Year 2014, corresponding to an estimate of 3-4 awards. The number of awards is contingent upon NIH appropriations and funds availability as well as the submission of a sufficient number of meritorious applications. Future year amounts will depend on annual appropriations.

 

Award Budget  

An applicant may request a budget for direct costs up to $700,000 per year.

 

Award Project Period   

An applicant may request a project period of up to five years.

Sincerely,

Ronald M. Atlas, Ph.D.

Chair, Public and Scientific Affairs Board

 
Social Networks American Society For Microbiology © 2013

 

Computational Biologist job posting at 10X technologies

Interesting job posting I just got sent by 10X technologies:

Computational Biologist

10X is looking for an outstanding individual to join its Computational Biology group. This person will: (1) lead the development of algorithms that form the core of 10X software and (2) define custom analyses to guide product development. This position is a unique opportunity to work on an exciting and novel form of Next Generation Sequencing (NGS) data that enables a wide array of previously unachievable applications. The ideal candidate will have an extremely strong background in algorithms and statistics and will be highly proficient in both generating novel algorithms and combining them with existing tools.

The right candidate must also have strong programming skills, and a keen interest in biology and working with real-world data. Strong interpersonal skills, a desire to understand customer needs and the ability to communicate results clearly are a must. This position will interact closely with colleagues in biochemistry, microfluidics and chemistry.

Key Responsibilities

  • Develop algorithms for novel NGS data across a number of novel applications
  • Develop custom analyses to asses and guide development of the core technology
  • Work with software team to commercialize algorithms products
  • Work with early customers to understand applications and requirements
  • Analyze internally generated sequencing data

    Desired Skills and Background

  • PhD in computer science, mathematics, computational/systems biology or related field
  • Extremely strong background in algorithms and statistics
  • Strong programming ability in Python (experience with C/C++ a significant plus)
  • Hands on experience with NGS data tools (e.g. bwa, samtools, GATK)
  • Creative problem solver who obsesses over novel applications of data
  • A deep intuition for the processes utilized by current NGS technologies
  • A combination of mathematical depth with a healthy respect for the imperfections

    inherent in real-world data

  • Highly independent
  • Ability to work in a fast-paced and quickly changing environment

    For more information, please contact jobs

10XCompBioJobDescription.pdf

Great use of metagenomic data: community wide adaptation signatures

OK I have been dreaming about doing something like this for many years.  One of the potentially most useful aspects of shotgun metagenomic data is that you get a sample of many/all members of a microbial community at once.  And then in theory one could look across different species and taxa and ask – do they all have similar adaptations in response to some sort of environmental pressure.  There have been a few papers on this over the last few years (e.g. check out this one from Muegge et al on Diet Driving Convergence in Gut Microbes).  But this new paper is really the type of thing I have been hoping to see: Environmental shaping of codon usage and functional adaptation across microbial communities.  Basically they looked at codon usage in organisms in different metagenomic samples and found major metagenome specific signatures, suggesting that different taxa were in essence converging on common codon usage.

The paper is definitely worth a look.

——–
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.

——–

Ewan Birney visiting Davis, speaking at the Genome Center next Wednesday (14th August)

Forwarding this announcement i just received

Ewan Birney, the Associate Directory of the European Bioinformatics Institute, is visiting UC Davis next Wednesday and will be giving a talk at 2:00 in the GBSF Auditorium: ‘Using outbred genetics to understand basic biological processes’.
He will also talk about the need for a data infrastructure in the life sciences and how the European Bioinformatics Institute contributes to it.

Ewan is the creator/co-creator of many popular bioinformatics tools (e.g. GeneWise, CRAM, Velvet, Pecan), and has had an enthusiastic involvement in many other genomics/bioinformatics projects (e.g. Pfam, BioPerl, Ensembl), not to mention taking a leading role in the human ENCODE project.

Lab tech (level 3ish) in population genetics looking for job in Davis

I have a friend of a friend who has almost 20 years of experience as a technician working in population genetics and forensics.  She has just moved to Davis and is looking for work, she came highly recommended from her previous lab.   If anyone knows of any position she might look at, or anyone to contact please let me know.  I can also send a resume on request.

News coverage of SpaceMicrobes event

Quick post here.  Our Project MERCCURI got some press coverage relating to an event July 20th with the Arizona Cardinals: Gilbert, Tempe participate in national microbe-swabbing project – East Valley Tribune: Gilbert.

From the article:

“The event — held at the Arizona Cardinals’ training facility on July 20 — featured members of the Cardinals’ cheerleading squad swabbing their shoes and cell phones to collect microbe samples later sent to a lab at the University of California Davis for analysis. Microbes are microscopic single-cell organisms that have existed for millions of years and are found just about everywhere on the planet.”

Also some mention of out sampling the Space Station and other parts of the project.

See more about the project 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.

——–

Perhaps this meeting should be renamed "Of Microbiomes and Men" ….

Well, just got an email inviting me to participate in a meeting on microbiomes. The full invite is at the bottom of this posting.  Alas, at first glances it seems this meeting, has, well, some gender issues.

Confirmed Keynote Speakers: both male.

  • Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
  • Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Confirmed other speakers: all seven male

  • Pierre Belichard, Co-founder and CEO, Enterome
  • Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
  • JunHua Li, Team Leader of Reference Metagenomics, BGI Research
  • Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
  • Steve Orndorff, NuMe Health
  • Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
  • Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus

I suppose one could say “Well, they are still working on their agenda … maybe they will have some female speakers.”  So I decided to dig around a little bit more. They provide a link to the outline agenda here. Alas that is even worse.  There we find out who some invited speakers are who have not yet accepted

  • David Odelson, R&D Program Director, Life Technologies
  • Peter B. DiLaura, President & CEO, Second Genome
  • Chris Christofferson, Morganthaler Ventures 
  • Lou Tartaglia, Third Rock Ventures
  • Mike Grey, Pappas Ventures
  • Justin L. Sonnenburg, Assistant Professor, Microbiology & Immunology, Stanford School of Medicine, Palo Alto, CA

So that is 9 confirmed speakers and six invited speakers – all of whom are male.  Great.  Here is a suggestion.  DO NOT GO TO THIS MEETING.

Microbiome Masthead
The Microbiome / Microbiota R&D and Business Collaboration Forum
Special August Registration Discount SAVE 15%

use discount code NN/AUG15/AL
Keynote speakers:
Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology
Dear Jonathan

The announcement in June that Johnson & Johnson is collaborating with Second Genome, one of the first biotech companies focused entirely on the human microbiome, is, according to Forbes magazine, a turning point at which “big Pharma” money begins to back this new field of research.

The 1-2 kilograms of bacteria living inside, and on the surface of, all human beings – the Human Microbiome – constitutes both another “human” organ and a third protective “immune system” after the innate and adaptive immune systems. This mix of good and bad bacteria, long a subject of academic interest, has been linked to everything from infectious diseases like clostridium difficile to obesity and even mental health. Now that the commercial potential of this field of research is being recognized it is attracting venture capital and other funding.

The developments in research and the commercial possibilities are the subject of The Microbiome/Microbiota R&D and Business Collaboration Forum, which will take place in San Diego onOctober 7th & 8th 2013.

Register today to secure the August 15% booking discount:
www.globalengage.co.uk/microbiome.html

Any questions? email nnoakes@globalengage.co.uk or telephone +44 (0)1865 849841
Confirmed Keynote Speakers


Mark Adams
Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego

Sarkis Mazmanian
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology
Confirmed Speakers


Pierre Belichard, Co-founder and CEO, Enterome
Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
JunHua Li, Team Leader of Reference Metagenomics, BGI Research
Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
Steve Orndorff, NuMe Health
Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus
This first-in-class, microbiome-focused hybrid R&D and business conference attracting 150 attendees from all over the world, plus an exceptional speaker faculty, will provide an interactive networking forum to both further research and commercialization opportunities.  It also aims to answer your queries through a vibrant exhibition room full of technology providers showcasing their R&D platforms & services; as well as via scientific poster sessions; expert-led case-study presentations; and interactive Q&A panel discussions.
The Outline Agenda


Sequencing/Bioinformatics of the Microbiome

  • An overview of the human microbiome project
  • Contributions to Metagenomics and Data Analysis
  • Advances in sequencing technologies
  • The role of chip technologies (the Phylo chip) as a rapid readout vs. sequencing
  • The $1000 genome may cost $100Ms to interpret!

Venture Capital + Technology Transfer

  • Commercializing Microbiome Technologies from Government & Academic Entities
  • International Small Company Showcase

The microbiome of the GI tract

  • The role of commensal bacteria in regulating the immune system
  • Metabolic exchange in gut microbial communities: who needs vitamins?
  • Contemplating novel antibiotic therapies that do not destroy the healthy microbiome
  • Metagenomic profiling in IBD

Clinical Applications

  • The contribution of the gut microbiome to liver disease
  • Treatment of C. Difficile infections with fecal transplants

Connections to the Food World

  • The role of diet in regulating the microbiome mix
  • Prebiotics vs. probiotics vs. pharmaceuticals
  • Opportunities to treat diabetes and obesity via the microbiome
  • Panel Discussion – Pharma/Biotech/Food Industry Partnering
  • Small Company Showcases
www.globalengage.co.uk/microbiome.html
Not interested in the Microbiome/Microbiota?
Unsubscribe here

Nick Noakes: nnoakes@globalengage.co.uk Tel +44 (0) 1865 849841
Global Engage, The Kidlington Centre, Kidlington, Oxfordshire, OX5 2DL, UK.

You might think that at some point some of the people organizing meetings

——–
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.

——–

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

Search for Executive Director, UCSD Center for Bioinformatics Analysis

Just got this by email. Seems like an interesting job —

———- Forwarded message ———-

Date: Tue, Jul 30, 2013 at 6:49 PM
Subject: Search for Executive Director, UCSD Center for Bioinformatics Analysis
To: jaeisen@ucdavis.edu
Dear Jonathan Eisen,

I am writing to seek your assistance in identying a director of a new center being established at UC San Diego, the Center for Bioinformatic Analysis. This center will establish a world-class program of bioinformatics research, collaboration and service. Its mission is to develop and apply technology for integrating diverse ‘omics data sets and to establish the means by which this information can be translated to the clinic to promote human health and prevent disease. To lead the Center for Bioinformatic Analysis we are looking for an Executive Director who has a PhD in Bioinformatics or related discipline with substantial team management experience in industry or academia. S/he will be responsible for the overall planning, function and long-term support of the Center. Key responsibilities involve interacting with UC San Diego life sciences faculty and engaging them in collaborative research projects; management of Center staff dedicated to collaboration or software development; reporting to UC San Diego faculty leadership and advisory boards; establishing the Center business model and lead in outreach and fundraising efforts. Under the leadership of the Director, the Center will be staffed by several dozen bioinformatics personnel that carry out the key functions of the center. I would greatly appreciate it if you could forward this notice and alert any candidates who might be interested. The job application is online at the UCSD web portal: http://jobs.ucsd.edu/bulletin/job.aspx?cat=search&sortby=rank&jobnum_in=67358&search=bioinformatics Thanks for your help!