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Open source code: https://github.com/chris-zen/wok

Source:https://bitbucket.org/bbglab/wok


Introduction

Wok is a workflow management system implemented in Python that makes very easy to structure the workflows, parallelize their execution and monitor its progress among other things. It is designed in a modular way allowing to adapt it to different infraestructures.
For the time being it is strongly focused on clusters implementing any DRMAA compatible resource manager (i.e. Oracle Grid Engine) which working nodes have a shared folder in common. Other, more flexible infrastructures (such as the Amazon EC2) are considered for future implementations.
Workflows in Wok are defined in an xml file with the .flow extension. This definition includes:
  • the different modules (or pieces of processing)
  • the interconnections between modules (i.e. the input of module B links with the output of module A)
  • explicit dependencies (i.e. module A cannot be executed until module B has finished)
  • descriptions that can be used to generate documentation automatically or to create web forms

Each module corresponds with a piece of software that has to be run in order to process some input and generate an output. For now, only Python scripts are allowed, but they can be used to execute software written in other languages.
Workflows in Wok can be treated as any software project and managed with version control system tools and the IDE of your choice.
Wok can be used as a terminal script or can be run in server mode.
The execution of a workflow in the terminal is done using the wok-run script which allows few options:
  • An instance name (-n name), which allows to run the same workflow many times simultaneously independently
  • Configuration files (-c file.conf), the configuration can be splitted in as much files as desired
  • Configuration parameters (-D param=value), which overwrite any previous configuration in configuration files

The workflow definition file (i.e. myworkflow.flow) is passed as the first argument.
To monitor the execution of the workflow there are different resources available:
  • The web server that allows to interact with the engine in a very straightforward way. Recommended!.
  • The logs emited by the wok-run through the standard output,
  • The intermediate files generated by Wok (i.e. the tasks output files)

It has been designed for workflow developers who feel more confortable programming than doing hundred of clicks and drag & drop's, and also for those who want infraestructure flexibility and full control and monitorization of the execution.

Authors


It is being developed by Christian Pérez-Llamas under the Biomedical Genomics Research Group.








The German Center for Neurodegenerative Diseases (DZNE) in Göttingen offers an open position for a postdoctoral bioinformatician in the 'Analysis of Biological Networks' group of Stefan Bonn.

The DZNE is a center of excellence within the Helmholtz Association that performs translational research on neurodegenerative diseases. The center includes nine high-performing sites in Berlin, Bonn, Dresden, Göttingen, Magdeburg, Munich, Rostock / Greifswald, Tübingen and Witten.

The successful candidate will work within a team of bioinformaticians in a multidisciplinary environment spanning bioinformatics and neuroscience. The work will focus on the development of novel algorithms and software for the integrative analyses of various genome-wide datasets derived from massively parallel sequencing (ChIP-, MeDIP-, RNA-, and small RNA-seq).

Candidates should have a strong background in bioinformatics, biostatistics or computer science, be looking for a collaborative and dynamic environment, and have a proven track record of productivity. Exposure to NGS analysis, parallel computing environments and machine learning is an asset but not a requirement.

The position is initially limited. Employment, payment and social benefits are determined by the Public Sector Collective Agreement (Tarifvertrag für den öffentlichen Dienst – TVöD). Job location is Göttingen, Germany.

The DZNE is an equal opportunity employer. The DZNE is committed to employing disabled individuals and especially encourages them to apply.

Applicants should send a letter of research interests, curriculum vitae, the names and contact details of two referees to Ulrike Kramer (Ulrike.Kramer@dzne.de). Please indicate 'Bioinformatics Postdoc' in the title of the e-mail.









The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. The advent of high-throughput, cost-effective methods for genotyping and sequencing has provided powerful tools that allow for the generation of the massive amount of genotypic data required to make these analyses possible.
dbGaP provides two levels of access - open and controlled - in order to allow broad release of non-sensitive data, while providing oversight and investigator accountability for sensitive data sets involving personal health information. Summaries of studies and the contents of measured variables as well as original study document text are generally available to the public, while access to individual-level data including phenotypic data tables and genotypes require varying levels of authorization.
The data in dbGaP will be pre-competitive, and will not be protected by intellectual property patents. Investigators who agree to the terms of dbGaP data use may not restrict other investigators' use of primary dbGaP data by filing intellectual property patents on it. However, the use of primary data from dbGaP to develop commercial products and tests to meet public health needs is encouraged.

Submission Policy

Submitters who are not Federally-funded and affiliated with an NIH IC will need to work with an NIH DAC so that proposed submission can be reviewed for consistency with appropriate policies to protect the privacy of research participants and confidentiality of their data. Submissions to dbGaP will not be accepted without assurance that the submitting institution approves the submission and has verified that the data submission is consistent with all applicable laws and regulations, as well as institutional policies. Submitters must also identify any limits on research uses of the data that are specifically set by individual research participants, e.g., through their informed consent.

Data Content and Organization

Open-Access Data
Open-access data can be browsed online or downloaded from dbGaP without prior permission or authorization. These data will include, but may not be limited to, the following:

dbGaP Data TypeWhere to Find It
Studies'Study' column when browsing studies
Result of a search under the tab 'Studies'
Part of the breadcrumb path of a variable or document
Study DocumentsLink from 'Browse Studies'
Link under 'Associated Documents' on study report
Result of a search under the tab 'Study Documents'
Phenotypic VariablesLink under 'Browse Studies'
Link under 'Associated Variables' on study report
Result of a search under the tab 'Variables'
Genotype-Phenotype AnalysesLink under 'Associated Analyses' on variable report
Link under 'Associated Analyses' on study report













About Us
In a nutshell... This is the place to find out about, take part in, and contribute to science through recreational activities and research projects. Learn more about citizen science.

If you're a scientist or a representative of a citizen science organization or community group: This is the place to tell eager people about your work and get them interested in helping out.

Our Mission
SciStarter will bring together the millions of citizen scientists in the world; the thousands of potential projects offered by researchers, organizations, and companies; and the resources, products, and services that enable citizens to pursue and enjoy these activities. 

We aim to:
Enable and encourage people to learn about, participate in, and contribute to science through both informal recreational activities and formal research efforts.
Inspire greater appreciation and promote a better understanding of science and technology among the general public.
Create a shared space where scientists can talk with citizens interested in working on or learning about their research projects.
Satisfy the popular urge to tinker, build, and explore by making it simple and fun for people—singles, parents, grandparents, kids—to jump in and get their hands dirty with science.

Our Team



Darlene Cavalier
Founder

Darlene is also the founder of Science Cheerleader  a popular website and organization that works with 250 current and former NFL and NBA cheerleaders pursuing science and technology careers to promote science and the involvement of citizens in science and science-related policy. She has held executive positions at Walt Disney Publishing and has worked at Discover magazine for 15 years, where she now is a senior adviser and writer. She has created national science awards programs, science education initiatives, and a series of science-themed roundtable discussions for, among others, the Disney Institute, Space.com, Sally Ride's Imaginary Lines, and the Franklin Institute. She also serves on the Steering Committee for Science Debate and is a founding partner of Expert and Citizen Assessment of Science and Technology, which engages experts, stakeholders, and everyday citizens in assessing the implications of emerging developments in science and technology. She originated and managed the Emmy award-winning Science of NFL Football series produced by the NFL, NBC Sports, NBC Learn, the National Science Foundation and Science Cheerleader.
A former Philadelphia 76ers cheerleader, Darlene does not regret the years she gabbed through high school science classes. She earned a Master's degree at the University of Pennsylvania, studying science history, sociology, and science policy to learn more about people like herself: "hybrid actors," citizens interested in but not formally trained in the sciences. Discovering it was remarkably difficult to find opportunities to participate in science in any meaningful way, she launched SciStarter. Darlene lives in Philadelphia with her husband and four children, who have made it a hobby to explore the rainforests of Costa Rica. She's also a faculty associate at Arizona State University where she teaches a graduate course, aptly titled, Citizen Science.


Lily Bui 

Executive Editor

Lily Bui holds dual degrees in International Studies and Spanish from the University of California Irvine. She has worked on Capitol Hill in Washington, D.C.; served in AmeriCorps in Montgomery County, Maryland; worked for a New York Times bestselling ghostwriter; and performed across the U.S. as a touring musician. She currently works in public media at WGBH-TV and the Public Radio Exchange (PRX) in Boston, MA. In her spare time, she thinks of cheesy science puns. Follow @dangerbui. 



Jenna Morgan Lang

Editor, Featured Projects and Newsletter

Dr. Jenna Lang spends her days exploring the various means by which microbes rule the world. She has worked with Jonathan Eisen since 2006, first as an employee of the DOE Joint Genome Institute, then as a Microbiology PhD student, and now as a permanent fixture in his lab at UC Davis. Jenna became hooked on Citizen Science while working with Darlene on Project MERCCURI, and now aims to include a citizen science component in all future research projects. For fun, she likes to play poker, at the Bellagio, in her wedding dress.



John Ohab

Contributor

Dr. John Ohab is a digital strategist at the U.S. Naval Research Laboratory. John was previously a new technology analyst at the Department of Defense  Public Web Program, providing research and evaluation of web technology initiatives. He also led Defense Department's award-winning outreach project, “Armed with Science,” a cross-agency effort to connect military scientists and engineers with the public through social media. John joined the government through consecutive American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellowships at the Department of Defense (2008) and the National Institute of Mental Health (2007). John received his B.S. in biopsychology from UC Santa Barbara in 2002 and his Ph.D. in neuroscience from UCLA in 2007. John was born and raised in Tempe, Arizona, experienced a moderately successful run in high school varsity tennis, and is waiting patiently for that elusive Arizona Cardinals Super Bowl victory.


Mark Severance

Director of Space-based citizen science projects

Mark Severance is SciStarter’s Space Guy and he has been a Space Guy all of his life. A NASA engineer at the Johnson Space Center in Houston, Mark has spent most of his career in Mission Control Center-Houston as a Flight Controller for the Space Shuttle and International Space Station. He also spent time in Mission Control Center-Moscow as a NASA Operations Lead early in the ISS program and when NASA had Astronauts working onboard the Mir space station. He has had a life-long interest in spaceflight and views the space program as a catalyst for engaging minds of all ages in a deeper understanding of science, engineering, technology and mathematics. Mark holds BS degrees in Physics and Electrical Engineering from SMU and MS in Physical Science, with a concentration in Orbital Mechanics, from the University of Houston. He began his hands on interest in space as teenager through his radio tracking of Soviet and Chinese human and robotic spacecraft in conjunction with the Kettering Group. He credits his satellite tracking as the most directive force in his educational and professional careers. Mark is currently a NASA engineer and manger for a space communications lab at the Johnson Space Center. Previous to this assignment, he worked in NASA’s Office of Education to start a program of educational activities and experiments onboard the ISS. He is heading up SciStarter’s in-development suite of space-related, citizen science projects.


Jonathan Brier

Strategic Advisor

Jonathan Brier is citizen science enthusiast from Michigan who enjoys working with Internet connected technologies a little too much. He holds a M.S. in Information and specialized in social computing from the University of Michigan School of Information and a B.S. in Media and Communication technologies from Michigan State University. His interest for science began with his continued use of the word “why” for which his father an engineer and mother a teacher took the time to give an explanation that would make any scientist proud. Jon’s citizen science passion began with his discovery of the SETI@home distributed computing project after watching the movie Contact. This branched to all things citizen science as he learned of more ways science research could harness public participation. Outside his day job as a User Experience Researcher at the University of Michigan, he works with GridRepublic on BOINC powered distributed computing projects and scours the Internet for anything and everything related to citizen science. He hopes to bring added enthusiasm and expertise to SciStarter.


Caren Cooper

Contributor

Dr. Caren Cooper is also a blogger for Scientific American and the Public Library of Science. She is a research associate at the Cornell Laboratory of Ornithology and Senior Fellow in the Environmental Leadership Program. She is co-chair of the publications committee of the newly forming Association for Citizen Science and co-editor of an upcoming special feature on citizen science in the open-access journal Ecology & Society. She has authored over 35 scientific papers, co-developed software to automate metrics of incubation rhythms, and is co-creator of NestWatch, CamClickr, Celebrate Urban Birds, YardMap, and the House Sparrow Project. Follow her @CoopSciScoop. She likes to propel herself on one wheel, two wheel, and eight wheel devices.



Nick Fordes

Contributor

Nick Fordes is a science enthusiast who enjoys doing, teaching, and communicating science.  Nick recently graduated from the University of Idaho with an M.S. in Water Resources.  His research involved creating a web-based participatory GIS application for use in watershed management. He has a true love for technology and appreciation for what the web-based communications can do for promoting science and increasing science literacy.   Nick most recently worked with the Council for Environmental Education, developing K-12 environmental science based curriculum.  In his spare time, Nick enjoys biking the bayous in Houston and fishing as often as he can.  He has been known to use his scientific knowledge to make a pretty mean brisket.



Lisa Gardiner

Contributor

Dr. Lisa Gardiner enjoys exploring the Earth from the tops of Colorado’s mountains to the bottom of tropical seas. She has a background in earth science, climate science, ecology, and paleontology - receiving her B.A. from Smith College in Geology and Marine Science and her Ph.D. from University of Georgia in Geology. She is currently honing her skills writing about science in the M.F.A. program at Goucher College. Lisa started Citizen Science Buzz, a blog on Talking Science to share exciting stories about how the public is getting involved with science. Lisa also develops resources for the public, students, and teachers to learn about the earth at Spark, UCAR Science Education. She has written for educational websites, led workshops for teachers, taught environmental education, and occasionally helped develop museum exhibits. She is the author and illustrator of several books and articles about science for children. For several years, Lisa’s eyes were glued to fossil coral reefs in the Bahamas as she searched for tiny clams and snails to study for her dissertation. Now she lives a mile above the ocean in Colorado and is a fan on hiking in summer, whether through mountain tundra or through city blocks, and skiing and snowshoeing in winter. When wearing her artist hat, Lisa creates painting of trees (or forests, depending on your perspective).


Pete Madden

Contributor


Pete Madden is a freelance journalist based in Los Angeles, California. He holds an M.S. in Digital Media from the Columbia Journalism School and a B.A. in Communication Studies and English from Vanderbilt University. He is currently Content Coordinator at Escape Apps, a tech startup that creates travel and local discovery smartphone apps, and he has worked for the Los Angeles Times, ABC World News with Diane Sawyer, and Regis High School, a tuition-free prep school in New York City. An avid swimmer and diver, Pete has been lucky enough to explore the reefs in Australia, Belize, and the Galapagos, and when he's not writing about citizen science, you can find him planning his next underwater adventure.











Description
A postdoctoral position is available in the laboratory of Dr. Adam Auton, in the Department of Genetics at Albert Einstein College of Medicine in New York, USA (http://autonlab.einstein.yu.edu/). Research goals of the lab are to use statistical methods in conjunction with high-throughput DNA sequencing to understand patterns of genetic diversity, and to quantify how these patterns vary across individuals. We are interested in a variety of problems, including investigation of the influence of mutation, recombination, and natural selection. Much of our current work is focused on humans and other mammals, but we are potentially interested in other organisms.
We welcome candidates with a demonstrated interest in genetics and evolution, with a background in Population and Statistical Genetics, Bioinformatics, Computer Science, or related disciplines. Strong programming skills are essential. Experience with high-throughput sequencing data and/or experimental techniques would be an advantage. Salary will be based on the NIH scale. Please email a CV including list of publications and names of two references to adam.auton@einstein.yu.edu. Informal inquiries are also welcome.








Job Description
The Mouse Genome Informatics program at The Jackson Laboratory in Bar Harbor, Maine, is seeking a Bioinformatics Analyst working with the Mouse Genome Database (MGD). MGD integrates a wide range of mouse genetic, genomic, and phenotypic data, including gene characterization, gene localization and sequence, vertebrate gene homologies, phenotype characteristics, allelic variants and mutants, and strain data.

The Bioinformatics Analyst will concentrate on functions necessary to bring regulatory elements into MGD. Work will include writing scripts for parsing data from external providers into defined file formats that can be uploaded into MGD and the GBrowse sequence viewer, writing scripts to automate assignment of regulatory elements with Sequence Ontology terms and to perform nomenclature quality checks. The Bioinformatics Analyst will work with data providers to ensure data representation consistency and work with software developers to automate annotation updates as revisions to the mouse genome reference assembly are released. Applicants should have a strong background in genome sequence analysis and demonstrated proficiency with scripting languages such as PERL or Python. Knowledge of community data format and sharing standards such as GFF and DAS is preferred.
Required Skills
Candidates should have excellent writing and communication skills and the ability to work effectively in a team environment. Ph.D. degree in Life Sciences highly preferred; exceptional individuals with M.S. degrees and extensive specific knowledge domain experience will be considered.


















Description
Research Highlights: Integrative Analysis of Multi-scale Sequencing Data towards better Understanding of Infectious Diseases, Host and Microbiome, and Control of Drug Resistance.
* Unique expertise in third generation sequencing (single molecule real-time) that can detect nearly twenty different types of DNA modifications and discover novel types
* Integration with 2nd-gen sequencing for functional/comparative epigenomics/genomics, transcriptomics, metabolomics
* Pathogen-host interactions in infectious and genetic (specifically mitochondrial) diseases
A postdoctoral research fellowship position is available at the Mount Sinai School of Medicine in New York City. Our lab is in the department of Genetics and Genomic Sciences and the Institute for Genomics and Multi-scale Biology, one of the top institute on computational biology in the nation. Our research emphasizes the biological and clinical impacts in the design of effective computational and statistical models. Successful candidates will have unique opportunities to take the lead roles in the use of single molecule real-time sequencing to better understand infectious diseases (bacteria, virus, fungi, parasites), mitochondrial diseases (neurodegenerative diseases and cancers) and drug resistance. Compensations for successful postdoc fellows are highly competitive.
Recent publications on these topics include:
* PLoS Genetics, 2013
* PLoS Computational Biology, 2013
* Nature Biotechnology, 2012
* Genome Research, 2012
Here are some of the specific questions that we are trying to answer in ongoing projects:
* How does DNA chemical modifications contribute to pathogen virulence, drug resistance and interaction with host and microbime?
* Are there methylations in mitochondrial DNA or just damages? Where are they? What are their functional roles in neurodegenerative diseases and cancers?
* How do genomic variations and epigenomic variations interact with each other in molecular and cellular regulation?
 To apply
Interested? Excited? Join us to reveal the cool biology! Candidates with PhD in computational biology, bioinformatics, computer science, or statistics with experience on analyzing biological and medical data are encouraged to apply. Solid computer programming, statistical, data mining, machine learning skills are desirable. Please send the following to gang.fang@mssm.edu
1) CV with a list of publications
2) A brief description of your previous research experience, best including any of the following three topics: sequencing data, GWAS or microbiome.
3) PDF files for the papers that involve computational and statistical data analyses, in which you are first or co-first author.
*Lab page with details*:http://research.mssm.edu/fanglab