Publish or Perish: The Future of Scholarly Communications and Academic Careers #PublishPerish14

Meeting about to start and thought I would post announcement here too.  Follow on Twitter at #PublishPerish14 

Scholarly publishing is in a bit of turmoil.  This upheaval impacts not only the dissemination of knowledge but also the assessment of scholars (and thus their careers).  For two days in February 2014 at UC Davis we will cover some of the key changes in scholarly publishing with a focus on how they impact the careers of academics.  Some key details of the meeting are summarized below:
  • Sessions topics will focus on changes occurring in scholarly publishing (in journal publishing, other forms of digital publishing, peer review, and economics of publishing) and on changes in assessment (alt metrics, assessment by institutions, and new models for evaluating scholars).
  • Each session of the meeting will include a mix of a keynote talk, short talks, and a panel discussion by leading experts in the field.  Ample time will be provided for discussions and networking as well.
  • In addition, at the end of Day 1 there will be a special Keynote talk by Yochai Benkler from Harvard University on ”Open Access, Cooperation, and Commons: The (Uncertain) Retreat of Possessive Individualism in Networked Society“ followed by a reception.
  • This meeting is organized by the UC Davis Innovating Communication in Scholarship (ICIS) Project (icis.ucdavis.edu), which is a collaboration between Mario Biagioli (UC Davis School of Law), Mackenzie Smith (UC Davis University Library) and Jonathan Eisen (UC Davis Genome Center).

Session Topics and Confirmed Speakers/Panel Participants
DAY 1: Thursday, Feb 13th
  • 8 – 8:30 am | Registration
  • 8:30 – 9 am | Welcoming Remarks
  • 9 – 10:30 am | Session 1 | The Changing Nature of the Journal
    • Heather Joseph, Scholarly Publishing and Academic Resources Coalition
    • John Inglis, Cold Spring Harbor Laboratory & BioRxiv
    • Chris Kelty, UCLA
    • Gregg Gordon, Social Science Research Network
  • 10:30 – 11 am | Coffee
  • 11 am – 12:30 pm | Session 2 | Beyond Journals & New Forms of Digital Publishing
    • Carly Strasser, California Digital Library
    • Carl Boettiger, ROpenSci
    • Erik Kansa, Alexandria Archive Institute & Open Context
    • Kaitlin Thaney, Mozilla Science Lab
  • 12:30 – 2 pm | Lunch
  • 2 – 3:30 pm | Session 3 | Innovations in Peer Review
    • Victoria Stodden, Columbia University
    • Emily Ford, Portland State University
    • Ivan Oransky, Retraction Watch & New York University
    • Cesar A. Berrios-Otero, Faculty of 1000
    • Jonathan Dugan, Public Library Of Science
  • 3:30 – 4 pm | Venue Shift & Coffee
    • Note venue shift to Buehler Alumni Center, AGR Room for keynote address
  • 4 – 6 pm | Buehler Alumni Center, AGR Room | Keynote Address*
    • Yochai Benkler, Harvard University on “Open Access, Cooperation, and Commons: The (Uncertain) Retreat of Possessive Individualism in Networked Society”
  • 6 – 7 pm | Reception*
* Hosted jointly with the Mellon Initiative on Digital Cultures & the Provost’s Forums on the Future of the Public University and the Social Good
DAY 2: Friday, Feb 14th
  • 9 – 9:45 am | Opening Talk
    • Diane Harley, Center for Studies in Higher Education & UC Berkeley, “Predicting the future of scholarly communication: faculty values, disciplinary cultures, and advancing careers”
  • 9:45 – 11:15 am | Session 4 | Changing the Value Proposition of Publishing
    • Greg Tananbaum, ScholarNext
    • Peter Binfield, PeerJ
    • Allison Fish, UC Davis
    • Todd Vision, Dryad & UNC Chapel Hill
  • 11:15 – 11:30 am | Coffee
  • 11:30 – 1 pm | Session 5 | Altmetrics: Do They Measure Anything Useful?
    • Molly McCarthy, UC Davis
    • Nettie Lagace, National Information Standards Organization
    • Anurag Acharya, Google Scholar
    • Jennifer Lin, Public Library Of Science
  • 1:00 – 2:30 pm | Lunch
  • 2:30 – 4:00 pm | Session 6 | Assessment
    • Linda Katehi, Chancellor, UC Davis
    • Sarah Greene, Rapid Science
    • Margie Ferguson, Modern Language Association & UC Davis
    • Kerry Ann O’ Meara, University of Maryland
    • Josh Rosenbloom,  STAR METRICS
  • 4 – 4:15 pm | Coffee Break
  • 4:15 – 5 pm | Closing Discussion | What we have learned, where we are now, & what we need to do next
    • Discussants: Yochai Benkler (Harvard), Mario Biagioli (UC Davis), Jonathan Eisen (UC Davis), Josh Greenberg (Sloan Foundation), Heather Joseph (SPARC), and MacKenzie Smith (UC Davis).
  • 5 – 6 pm | Bonus Session | Lightning Talks

The Life Sciences Podcast on #OpenAccess

Quick post here.  There is a new podcast that may be of interest Episode 8: The open access debate | The Life Sciences Podcast.  From the Faculty of Life Science of the University of Manchester – they interviewed me, Alicia Wise from Elsevier, two librarians – Jan Wilkinson and Simon Bains and Andrea Baier from the British Ecological Survey and discuss multiple issues associated with open access publishing.

Announcement: CFP: The Contours of Algorithmic Life conference @ UC Davis

Got this by email and seemed of possible interest though it is not what I expected based on the title.

CFP: The Contours of Algorithmic Life

A conference sponsored by The Mellon Research Initiative in Digital Cultures
May 15-16, 2014 at the University of California, Davis

Submission Deadline: March 1, 2014
Send submissions to algorithmiclife

As algorithms permeate our lived experience, the boundaries and borderlands of what can and cannot be adapted, translated, or incorporated into algorithmic thinking become a space of contention. The principle of the algorithm, or the specification of the potential space of action, creates the notion of a universal mode of specification of all life, leading to discourses on empowerment, efficiency, openness, and inclusivity. But algorithms are ultimately only able to make intelligible and valuable that which can be discretized, quantified, operationalized, proceduralized, and gamified, and this limited domain makes algorithms necessarily exclusive.

Algorithms increasingly shape our world, our thought, our economy, our political life, and our bodies. The algorithmic response of NSA networks to threatening network activity increasingly brings privacy and political surveillance under algorithmic control. At least 30% of stock trading is now algorithmic and automatic, having already lead to
several otherwise inexplicable collapses and booms. Devices such as the Fitbit and the NikeFuel suggest that the body is incomplete without a technological supplement, treating ‘health’ as a quantifiable output dependent on quantifiable inputs. The logic of
gamification, which finds increasing traction in educational and pedagogical contexts, asserts that the world is not only renderable as winnable or losable, but is in fact better–i.e. more effective–this way. The increased proliferation of how-to guides, from HGTV and DIY television to the LifeHack website, demonstrate a growing demand for
approaching tasks with discrete algorithmic instructions.

This conference seeks to explore both the specific uses of algorithms and algorithmic culture more broadly, including topics such as: gamification, the computational self, data mining and visualization, the politics of algorithms, surveillance, mobile and locative technology, and games for health. While virtually any discipline could have something productive to say about the matter, we are especially
seeking contributions from software studies, critical code studies, performance studies, cultural and media studies, anthropology, the humanities, and social sciences, as well as visual art, music, sound studies and performance. Proposals for experimental/hybrid
performance-papers and multimedia artworks are especially welcome.

Areas open for exploration include but are not limited to: daily life in algorithmic culture; gamification of education, health, politics, arts, and other social arenas; the life and death of big data and data visualization; identity politics and the quantification of selves, bodies, and populations; algorithm and affect; visual culture of algorithms; algorithmic materiality; governance, regulation, and ethics of algorithms, procedures, and protocols; algorithmic imaginaries in fiction, film, video games, and other media; algorithmic culture and (dis)ability; habit and addiction as
biological algorithms; the unrule-able/unruly in the (post)digital age; limits and possibilities of emergence; algorithmic and proto-algorithmic compositional methods (e.g., serialism, Baroque fugue); algorithms and (il)legibility; and the unalgorithmic.

For more information, especially on updates regarding featured keynote speakers and performers, check out the conference website at: algorithmiclife.ucdavis.edu

Please send proposals of no more than 250 words to algorithmiclife by March 1, 2014.

Decisions will be made by March 8, 2014.

Nice collection in IJSEM on Integrating genomics into Microbial Systematics

Nice collection in IJSEM worth looking at.  The overview is particularly useful

Overview:

Other papers 

DOE-JGI Call for LOIs for Large-Scale Genomics Proposals due April 10, 2014

The DOE Joint Genome Institute (DOE JGI) Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. Priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities. The CSP data is immediately made publicly available, without exception.

A summary of the 2015 CSP Call is below. The full Call can be found here:

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants: Emphasis will be on proposals related to DOE JGI’s “flagship” plant genomes, including poplar, sorghum, Brachypodium, Chlamydomonas, soybean, foxtail millet, Physcomitrella, switchgrass, and miscanthus. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. Projects may fall into the following categories:

a) Gene Atlas and ENCODE-like projects;

b) Large-scale resequencing projects;

c) Plant microbiomes.

II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria &Archaea (GEBA) and 1000 FungalGenomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are encouraged that extend this effort using high-throughput sequencing, and the DOE JGI’s DNA synthesis capabilities and are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics that could serve as model organisms for DOE-relevant problems are encouraged and could include new DOE JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.

III. Microbial emission and capture of greenhouse gases in terrestrial systems: Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction through gene/genome engineering.

IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: The DOE JGI has developed a platform that enables the discovery of novel natural products based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics.

Deadlines

Letters of intent (LOI) will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/.

· LOI due: April 10, 2014

· Full proposals invited: April 24, 2014

· Full proposals due: June 5, 2014

· Projects begin: October 2014

Questions? Contact:

Axel Visel (avisel), DOE JGI Strategic Planning-Science Lead.



"Phylogeny driven approaches to genomics and metagenomics": slides w/ audio from my talk at #UCDavis 1/29

Gave a talk here at UC Davis last week. Alas, not my best talk – too rushed. But, anyway, here is a video of the slideshow w/ audio. Title “Phylogeny driven approaches to genomics and metagenomics”

 

Quick post – Outbreaker and the "Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data"

Interesting new paper out: PLOS Computational Biology: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data.

Full Citation:  Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, et al. (2014) Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLoS Comput Biol 10(1): e1003457. doi:10.1371/journal.pcbi.1003457

Abstract:

Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees (“who infected whom”) from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic approaches having been explored to date. We introduce a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks. Our approach identifies likely transmission events and infers dates of infections, unobserved cases and separate introductions of the disease. It also proves useful for inferring numbers of secondary infections and identifying heterogeneous infectivity and super-spreaders. After testing our approach using simulations, we illustrate the method with the analysis of the beginning of the 2003 Singaporean outbreak of Severe Acute Respiratory Syndrome (SARS), providing new insights into the early stage of this epidemic. Our approach is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker. It is applicable to various densely sampled epidemics, and improves previous approaches by detecting unobserved and imported cases, as well as allowing multiple introductions of the pathogen. Because of its generality, we believe this method will become a tool of choice for the analysis of densely sampled disease outbreaks, and will form a rigorous framework for subsequent methodological developments.

Check out the nice figure on a SARS outbreak:

Figure 5. Results of the analysis of the SARS data using outbreaker. This figure summarizes the reconstruction of the outbreak, showing putative transmissions (arrows) amongst individuals (rows). Arrows represent ancestries with a least 5% of support in the posterior distributions, while boxes correspond to the posterior distributions of the infection dates. Arrows are annotated by number of mutations and posterior support of the ancestries, and colored by numbers of mutations, with lighter shades of grey for larger genetic distances. The actual sequence collection dates are plotted as plain black dots. Bubbles are used to represent the generation time distribution, with larger disks used for greater infectivity. Shades of blue indicate the degree of certainty for inferring the origin of different cases, as measured by the entropy of ancestries (see methods and equation 12): blue represents conclusive identification of the ancestor of the case (low entropy), while grey shades are uncertain (high entropy).

And then the consensus transmission tree

Figure 6. Consensus transmission tree reconstruction of the SARS outbreak. This figure indicates the most supported transmission tree reconstructed by outbreaker. Cases are represented by spheres colored according to their collection dates. Edges are colored according to the corresponding numbers of mutations, with lighter shades of grey for larger numbers. Edge annotations indicate numbers of mutations and frequencies of the ancestries in the posterior samples.

Outbreaker is available here: http://cran.r-project.org/web/packages/outbreaker/index.html

I also like the 1st line of their Acknowledgements:

We are thankful to Sourceforge (http://sourceforge.net/) and CRAN (http://cran.r-project.org/) for providing great resources for developing and hosting outbreaker.

Definitely worth checking out.

The Quest for a Field Guide to the Microbes: talk at "Science in the River City"

I got invited a while back to give a talk at a “Science in the River City” workshop for 3rd – 12th grade science teachers.  I proposed (and they said yes) to the idea of talking about my “Quest for A Field Guide to the Microbes.”  I recorded the screen (slides) and audio from my talk using Camtasia and have now posted the slideshow and slides.  Here they are:

Talk slideshow with Audio on Youtube:

 

 Slides on Slideshare

Workshop at #UCDavis 3/24 From Science to Storytelling: Effective Communication for Policy Change

From Science to Storytelling: Effective Communication for Policy Change

Conveying the results of your scientific research to legislators and government agencies can help influence policy – but only if you communicate effectively! If you are motivated in part by applying your research to environmental and social issues such as climate change, this workshop will give you some useful concepts and tools. Using discussion, role plays, expert advice from media consultants and individual exercises, we will explore the challenges of translating your scientific findings to policymakers and advocates, and will offer some tools for improving your communications skills. We will focus on simplifying your messages and honing your presentations.

Invited participants:

Academic researchers working on climate change and agriculture. Registered participants may also invite one graduate student.

Organizers:

California Climate and Agriculture Network (CalCAN) and Resource Media

Date, time, location:

March 24, 1:00 – 4:00

Big Hanna Room, Asmundson Hall, UC Davis

Cost: Free

To register: Email Renata Brillinger at CalCAN (renata@calclimateag.org) with your name, department, institution and phone number. If you would like to bring one graduate student, please include their information as well. Space is limited.

Science Communication workshop 3-24-14.pdf

Using Social Media to Promote Your Research (workshop)

I’ll be running a social media workshop next Friday in the Genome Center – anyone on campus is welcome to attend! Details as follows:

Using Social Media
to Promote Your Research

Friday, February 7, 2014
12:30-2:30pm
Room 4202, Genome Center

Many view social media as either a fun distraction, a waste of time – or both!  But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

  • Use social media to share and promote your research
  • Identify appropriate audiences and avoid pitfalls
  • Choose the right platforms to help you achieve your goals

Please pre-register using this online form: http://bit.ly/1ajX6Pc (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

PDF Flyer available here