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Events: NCBI Hackathon
Submitted by Urska C; posted on Saturday, February 13, 2016
March 21-23, 2016
Note the short registration deadline of 2/19/2016!
Shreveport, LA, USA

Please, consider participating in this exciting event that will be hosted outside of NIH for the first time!

NCBI to assist Louisiana State University in South and Southeast regional genomics hackathon

From March 21st to 23rd, NCBI will assist Louisiana State University (LSU) in hosting a regional genomics hackathon in Shreveport, LA. This event is for students, postdocs, investigators and other researchers already engaged in the use of pipelines for genomic analyses from next-generation sequencing data or metadata (some projects are available to other non-scientific developers, mathematicians or librarians). Researchers and/or data scientists from the South and Southeast United States are especially encouraged to apply, but the event is open to anyone selected for the hackathon and able to travel to Shreveport.

Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. The potential subjects for this iteration are:

* Network Analysis of Variants
* Structural Variation
* RNA-Seq
* Streaming Data and Metadata
* Neuroscience/Immunity
* Command-line user-interface design

Please see the application for specific team projects.

After a brief organizational session, teams will spend three days analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems. This course will take place at the Louisiana State Health Sciences Center - Shreveport in Shreveport, Louisiana and is hosted by the two LSU institutions in town: LSU Health Sciences Center and LSU Shreveport.

Datasets will come from the public repositories housed at the NCBI. During the course, participants will have an opportunity to include other datasets and tools for analysis. Please note, if you use your own data during the course, we ask that you submit it to a public database within six months of the end of the event.

All pipelines and other scripts, software and programs generated in this course will be added to a public GitHub repository designed for that purpose. A manuscript outlining the design and usage of the software tools constructed by each team will be submitted to an appropriate journal.

To apply, complete this form, which takes approximately 10 minutes to complete. Applications are due February 2/19/16 by 5 pm ET. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior students and applicants are encouraged to reapply. Accepted applicants will be notified on February 22 by 2 pm ET, and have until February 26 at 9 am to confirm their participation. If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other data scientists from attending this event. Please include a monitored email address, in case there are follow-up questions.

Note: Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python) is necessary to be successful in this event. Employment of higher level scripting or programming languages may also be useful. Applicants must be willing to commit to all three days of the event. No financial support for travel, lodging or meals is available for this event. Also note that the course may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.
Please contact ben.busby[at] with any questions. Finally, if you are interested in having NCBI facilitate a regional hackathon hosted at your institution, please fill out this form.

Etc.: Voting commences for the 2016 Benjamin Franklin Award
Submitted by J.W. Bizzaro; posted on Wednesday, February 10, 2016
Submitter The members have selected the nominees for the 2016 Benjamin Franklin Award in the Life Sciences. This will be the 15th presentation of the humanitarian and bioethics award, given annually to an individual who has worked to promote open access to the materials and methods used in the life sciences.

The ceremony for the presentation of the award will be held at the 2016 Bio-IT World Conference & Expo in Boston ( It involves a short introduction, the presentation of the certificate, and the laureate seminar.

An online ballot and more information on the award can be found at An email ballot will also be sent directly to members.

Here are the nominees:

* Gary Bader, The Donnelly Centre, University of Toronto

Gary Bader ( is leading a group in computational biology at the University of Toronto and has promoted community efforts for a long time. As a Ph.D. student, he developed the Biomolecular Interaction Network Database (BIND) (, one of the first of dozens of molecular interaction databases. He also plays an active role in the development of open-source biological pathway and network data exchange formats, including PSI-MI ([link]) and BioPAX (; databases such as cPath (, Cancer Cell Map ( and Pathway Commons (; and visualization and analysis software such as Cytoscape (

* Benjamin Langmead, Johns Hopkins University

Ben Langmead ( is one of the most influential and highly cited authors of open source bioinformatics software. His Bowtie read alignment tool and its sequel Bowtie 2 ([link]) are widely used, with more than 10,000 citations between them, and they are used within more than 50 other software tools. Ben also has a series of publications on open source cloud-enabled tools that have collectively pushed back the frontier of what everyday biological researchers can do with large sequencing datasets. All of Ben's software, and all the software from his lab, are free and open source. He has also made available a large collection of open teaching resources that have become very popular ([link]).

* Aaron Quinlan, University of Utah

Aaron Quinlan ( is a longtime contributor of open source software, going back to the early days of next-generation sequencing. Open source software tools authored by Aaron and his lab members include Gemini (, BEDTools (, Lumpy (, and many others.

* Torsten Schwede, Swiss Institute of Bioinformatics and University of Basel

Torsten Schwede ([link]) has been a champion in bringing the modeling community together and in making protein models easily accessible to everyone. In the 1990s, Torsten first started working with others on the SWISS-MODEL modeling platform and repository (SMR, It is still one of the most widely used modeling servers to date, helping thousands of researchers per month. In 2007, he established the Protein Model Portal ( Torsten also produced two public access tools: CAMEO (, a server that allows developers to continuously evaluate the accuracy and reliability of their predictions; and Model Archive (, the first public repository for in silico structural models.

* Thomas Wu, Genentech

Thomas Wu ([link]) developed the GMAP and GSNAP ( short read aligners in 2005 and made it publicly available to anyone, and he continues to develop and support this software tirelessly. GSNAP is a complex, flexible and reliable aligner which is supported largely by this one person working at a for-profit institution -- a credit to both him and his company, Genentech.

Submitter EXCERPT:
These remains have been studied extensively, but the sequencing of their DNA is a major achievement, the researchers said. In their paper, they called this "the first snapshot of British genomes in the early centuries A.D." [Matthew] Collins said that the researchers couldn't have attempted such a feat when the skeletons were first discovered because the approximate cost would have been about $70 million. (With technological advances, the cost of such analyses has gone down, according to the Human Genome Project.)

Collins noted that the work exemplifies a new stage in archaeology. "The excitement is, we are now technologically able to do this kind of work, which is mind-boggling when you consider the great achievement of sequencing the first human genome was less than 15 years ago, and now we can sequence the genomes of Romans from York and Anglo-Saxons in Cambridge," Collins said. "It's just absolutely extraordinary."



Submitter EXCERPT:
The lead authors stressed that their findings, which combine basic science with large-scale analysis of genetic studies, depended on an unusual level of cooperation among experts in genetics, molecular biology, developmental neurobiology and immunology.

"This could not have been done five years ago," said Hyman. "This required the ability to reference a very large dataset .... When I was [NIMH] director, people really resisted collaborating. They were still in the Pharaoh era. They wanted to be buried with their data."


[link] (subscription required)

Submitter We are pleased to announce another web service from our group, developed for protein annotation using a structure in PDB.



Education: International Synthetic and Systems Biology Summer School
Submitted by Renato Umeton; posted on Tuesday, January 26, 2016
Submitter July 8-14, 2016
Volterra (Pisa), Tuscany, Italy

* Yaakov (Kobi) Benenson, Synthetic Biology Group[at]Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
* Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA
* Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy
* J. Gootenberg, Feng Zhang's Group, Department of Systems Biology, Harvard Medical School, Harvard University, USA
* Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark
* Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel
* Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy

More speakers will be announced soon!

Industrial Panel - TBA
Workshop on Next Generation Sequencing - Speakers TBA

Application: March 31, 2016
Notification Acceptance: April 10, 2016
Oral Presentation/Poster Submission: March 31, 2016
Notification of Decision for Oral/Poster Presentation: April 10, 2016

Submitter EXCERPT:
UT Southwestern Medical Center researchers have been awarded $3.6 million in NASA funds to study how space radiation would affect the cancer risk of astronauts taking part in deep space missions to Mars.

Dr. Sandeep Burma, Associate Professor of Radiation Oncology, will examine the increased risk of a highly malignant type of brain cancer called glioblastoma following exposure to particle radiation. Dr. Jerry Shay, Professor of Cell Biology, will study whether a drug known as CDDO administered before exposure to particle radiation reduces the risk of lung cancer and colon cancer.
"I think it's important for America to have vision, to be forward-looking, and that's something that NASA does for us," said Dr. Shay.


Submitter EXCERPT:
"We're watching our demise in real time," Lance Price, PhD, a prominent resistance microbiologist and founder of the Antibiotic Resistance Action Center at George Washington University, who not involved in any of the research, told me. "I guess this is one of the advantages of next-generation DNA sequencing, is we can watch ourselves fall apart."


Education: 2016 workshops
Submitted by Ann Meyer; posted on Monday, January 11, 2016 is is pleased to present the 2016 Canadian Bioinformatics Workshops series which are an advanced bioinformatic workshops. Please join us in another successful year.

New for 2016:
* Workshops will be offered in Vancouver, Toronto and Montréal
* Travel and registration awards will be available to eligible successful applicant students
* Enhanced networking opportunities to help you create a network with people working in the same research area
* Back-to-back workshops for better skill extension and application
* Three new workshops this year: Epigenomics, Population Genomics and Cloud Computing

The CBW is pleased to be offering the following advanced training opportunities in 2016:
* Informatics and Statistics for Metabolomics: Toronto, May 26-27, 2016
* Bioinformatics for Cancer Genomics: Toronto, May 30 - June 3, 2016
* Introduction to R: Toronto, June 6, 2016
* Exploratory Analysis of Biological Data using R: Toronto, June 7-8, 2016
* Informatics on High-throughpuut Sequencing Data: Montreal, June 9-10, 2016
* Pathway and Network Analysis of -omics Data: Toronto, June 13-15, 2016
* Informatics for RNA-seq Analysis: Toronto, June 16-17, 2016
* Epigenomic Data Analysis: Toronto, June 20-21, 2016
* Analysis of Metagenomic Data: Vancouver, June 22-24, 2016
* Bioinformatics on Big Data: Computing on the Human Genome: Toronto, July 14-15, 2016
* Population and Quantitative Genomics: Toronto, July 18-19, 2016

A link to the full program poster can be found at:

Looking forward to seeing you in 2016.

PS material from 2015 ((and others years) is on-line with a CC-BY-SA license:

Submitter EXCERPT:
About 2% of the DNA in most people alive today came from trysts between ancient humans and their Neanderthal neighbors tens of thousands of years ago, recent studies have shown. Now, scientists are trying to determine what, if any, impact that Neanderthal genetic legacy has on our contemporary lives.

In a pair of papers published this week in the American Journal of Human Genetics, two research teams report that in many people, a group of genes that govern the first line of defense against pathogens was probably inherited from Neanderthals.

These same genes appear to play a role in some people's allergic reaction to things like pollen and pet fur as well, the scientists said.


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