Friday, February 21st
Dr. Tanja Woyke from JGI.
"Genomics of uncultivated microorganisms by single-cell sequencing".
10AM in 1005 GBSF – the main auditorium.
Category: Misc.
Must read of the month: Show Me the Policy (on diversity at conferences)
Quick post here:
As many know I am a bit obsessed with the issue of gender balance at conferences. And thus I was so happy to read the following post: show me the policy | cubist crystal. It details how one can help improve diversity at meetings by making sure meeting organizers have a diversity policy in place. It even gives suggested wording to answer invitations. It has links to sites with information about diversity at meetings and links to other sites trying to collate information about meetings and their diversity. The post is by Jenny Martin – a structural biologist and it should be required reading for all academics.
Hat tip to Karen James for pointing me to this.
Another good one by @JennyMartin_UQ: ‘Show me the policy’, on conf. gender balance. http://t.co/AsC6pykNdD cc @phylogenomics #ripplesofdoubt
— Karen James (@kejames) February 17, 2014
//platform.twitter.com/widgets.js
Share this:
STEM Women: How Men Can Help, w/ Professor Jonathan Eisen (hey, that’s me)
Just got done with an interview “STEM Women: How Men Can Help, with Professor Jonathan Eisen” done via Google Hangout with Buddhini Samarasinghe and Zuleyka Zavallos.
Video of the chat has been posted to Youtube.
And there is a Google Plus Event Page here.
Share this:
Storify Summary of Day2 of #PublishPerish14
Another quick post here. I am working on a web site summarizing everything from our recent meeting we hosted at UC Davis:
To capture what was going on on Twitter I used Storify to make a summary of Day 2.
See below.
//storify.com/phylogenomics/publish-or-perish-meeting-at-ucdavis-day-2/embed//storify.com/phylogenomics/publish-or-perish-meeting-at-ucdavis-day-2.js[View the story “Publish or Perish #PublishPerish14 meeting at #UCDavis Day 2” on Storify]
Share this:
#UCDavis Genome Center Looking for a Manager for the DNA Technologies Core
UC Davis Genome Center Looking for a Manager for the DNA Technologies Core
Manager of the DNA Technologies and Expression Analysis Cores, (Academic Administrator V)
The Genome Center, UC Davis
The UC Davis Genome Center integrates experimental and computational approaches to address key biological problems in genomics. The Genome Center has five service cores that operate on a recharge basis to provide diverse research groups on and off campus with access to state–of-the-art technologies and technical staff on an at-cost, as-needed basis. The DNA Technologies and Expression Analysis Cores provide a broad range of services with particular emphasis on high-throughput DNA sequencing, SNP genotyping, and expression analysis. More details can be found at
https://recruit.ucdavis.edu/apply/JPF00219.
The Genome Center invites applications for the position of CoreManagerwho will have responsibility for the development and day-to-day running of the DNA Technologies and Expression Analysis Service Cores of the Genome Center. These responsibilities include but are not limited to advising researchers on project design, data interpretation, supervision of core staff, operation of the cores’ instrumentation, evaluation and development of new protocols, oversight of the cores’ finances, and conducting courses to enable researchers to use the cores’ technologies.
This position requires a Ph.D. in Molecular Biology, Biochemistry, Genetics, Chemistry, or related field with at least four years of postdoctoral experience. The individual should have knowledge and experience in molecular biology as reflected in his/her publication record. Demonstrated experience in running a service unit and supervising staff is required. The incumbent must possess broad chemical, biochemical, computational, and technical knowledge sufficient to supervise technical staff, troubleshoot problems, refine technologies, and advise researchers. The position is open until filled. Applications should be completed by February 22nd, 2014 to ensure full consideration. Applicants should apply on-line with names for at least three letters of recommendation at https://recruit.ucdavis.edu/apply/JPF00219.
The University of California is an affirmative action/equal opportunity employer
DNA Manager advert updated 021414 RWM.doc
Share this:
Valentine’s Day Seminar at #UCDavis: Herbert M Sauro: Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer.
The Genome Center Biological Networks Seminars Series present:
Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer.
Speaker: Herbert M Sauro
Associate Professor
Department of Bioengineering
University of Washington
Date: Friday, February 14th, 2014, 10am – 11pm
Location: 1005 GBSF
Abstract:
Reproducibility has been and is becoming more of an issue as the research we do becomes more complex. In the work I do there are two areas that warrant concern. The first is that the computational experiments we publish as a community are rarely if ever reproducible. Secondly, in synthetic biology where we design new organisms which are are also published we again are confronted with the fact that the bulk of published synthetic biology designs can not be recreated without recourse to the original constructs themselves. Sometimes even then the reported experiments cannot be reproduced. Reproducibility is at the heart of the scientific method and it damages science, particularly in the eyes of the general public, if the work we do cannot be easily reproduced. In addition, there are cost concerns when it can take months of labor to recreate work already done. The good news is that, at least in computational science, the reason for the lack of reproducibility is due almost entirely to human error. This is likely to true in experimental science as well. Human error can in theory be easily corrected. In this talk I will discuss some of the efforts going in my lab and others in relation to reproducibility in computational modeling and the design and implementing of synthetic organisms.
Share this:
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:
Session Topics and Confirmed Speakers/Panel Participants
DAY 1: Thursday, Feb 13th
* 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
Share this:
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.
Share this:
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.
Share this:
Nice collection in IJSEM on Integrating genomics into Microbial Systematics
Nice collection in IJSEM worth looking at. The overview is particularly useful
Overview:
- Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea by Jongsik Chun and Fred A. Rainey
Other papers
- Use of gene sequence analyses and genome comparisons for yeast systematics by Cletus P. Kurtzman
- Applications of next-generation sequencing to unravelling the evolutionary history of algae by Kyeong Mi Kim, Jun-Hyung Park, Debashish Bhattacharya, and Hwan Su Yoon
- Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes by Mincheol Kim, Hyun-Seok Oh, Sang-Cheol Park, and Jongsik Chun
- Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age by Jan P. Meier-Kolthoff, Hans-Peter Klenk, and Markus Göker
- Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria by Hafiz Sohail Naushad, Brian Lee, and Radhey S. Gupta
- A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species by Dhamodharan Ramasamy, Ajay Kumar Mishra, Jean-Christophe Lagier, Roshan Padhmanabhan, Morgane Rossi, Erwin Sentausa, Didier Raoult, and Pierre-Edouard Fournier
