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Newsletter Archives
10.16
No. 8: Visit GeneLab this fall at your favorite conference: ASGSR, AMIA and ASCB

Greetings From GeneLab!

GENELAB WORKSHOPS - AMERICAN SOCIETY FOR GRAVITATIONAL BIOLOGY (ASGSR) ANNUAL MEETING

GeneLab will be hosting two sessions at the 2016 ASGSR Annual Meeting to be held in Cleveland, Ohio October 26-29. On Thursday October 27, from noon to 2:00 p.m. EDT, GeneLab will present a plenary session with updates about the GeneLab project and scientific talks that highlight data in the GeneLab Data Repository. A "grab-and-go" lunch will be available onsite for purchase before the session. On Friday, October 28, from 1:30 to 3:00 p.m. EDT, members of the GeneLab team will present a tutorial on how to use the GeneLab Data System, how to submit data, data curation/metadata/standards, current vs. future capabilities, and GeneLab collaborations. Bring your questions and feedback. Both sessions will be webcast; instructions for how to participate in the webcast are here. The webcasts will be archived on the ASGSR website after the meeting.

GeneLab team members will present three posters at the ASGSR meeting:

GeneLab will co-host an information booth with NASA's Space Biology program. Stop by the booth for a hands on demonstration of the GeneLab data system, to meet our team members, or to ask questions about any other aspect of the GeneLab project.

A full schedule of all our activities at ASGSR is available here.

AMERICAN MEDICAL INFORMATICS ASSOCIATION (AMIA) ANNUAL SYMPOSIUM

AMIA is the professional society for health sciences informaticians. At the AMIA annual symposium to be held in Chicago, November 12-16, 2016, GeneLab's Dr. Dan Berrios will present a poster entitled NASA’s GeneLab: Phase One Results and Plan. Dr. Berrios' co-authors are Jon D. Welch, Homer W. Fogle, Michael Skidmore, and Oana Marcu. GeneLab will also be hosting an informational booth at the conference.

AMERICAN SOCIETY FOR CELL BIOLOGY (ASCB) ANNUAL MEETING

The ASCB annual meeting is the largest gathering of leading cell biologists worldwide. ASCB 2016 will be held December 3-7, 2016 in San Francisco, California. GeneLab will co-host an informational booth with the NASA Space Biology Program and Dr. Sigrid Reinsch will present a poster entitled GeneLab: Scientific partnerships and an open-access database to maximize usage of omics data from space biology experiments. Dr. Reinsch's co-authors are Jonathan Galazka, Dan Berrios, Kaushik Chakravarty, Homer Fogle, San-huei Lai, Valery Boyko, Linda Timucin, Peter Tran, and Mike Skidmore.

DO YOU HAVE A PUBLICATION THAT CITES GENELAB?

We would like to know! Please send us your citation so that we can include it in our metrics and post it on the GeneLab website. genelab-outreach@lists.nasa.gov

Sincerely,
The GeneLab Team

09.16
No. 7: New datasets, conference news

Greetings From GeneLab!

DATA RELEASES

Since our last newsletter, we've had two releases of datasets. The July 10 data release included six datasets from NASA's Space Biology Microbial Observatory project led by Kasthuri Venkateswaran, Ph.D., of NASA Jet Propulsion Laboratory and the California Institute of Technology. The data in these studies are only released through GeneLab. The September 21, data release comprised thirteen "legacy" studies that represent data previously published elsewhere, which are now curated in the GeneLab database. To view the announcement summary page for all new datasets, click this link - Data Release Announcements. The direct link to the data system is https://genelab-data.ndc.nasa.gov/genelab/.

GENELAB WORKSHOP - AMERICAN SOCIETY FOR GRAVITATIONAL BIOLOGY

GeneLab will host two sessions at the upcoming 2016 ASGSR Annual Meeting in Cleveland, Ohio on October 26-29. On Thursday October 27, from noon to 2:00 p.m.(EDT), GeneLab will present a plenary session with updates about the GeneLab program and scientific talks that highlight data in the GeneLab Data Repository. On Friday, October 28, from 1:30 to 3:00 p.m.(EDT), members of the GeneLab team will present a tutorial on how to use the GeneLab Data System, how to submit data, curation/metadata/standards, current and future capabilities and timeline, and collaborations. Both sessions will be webcast. Bring your questions and feedback. A more formal schedule of both sessions will be released soon and a brief announcement will be emailed to newsletter subscribers at that time.

Look for GeneLab at these other upcoming events

  • American Medical Informatics Association (AMIA) 2016 Annual Symposium
    Chicago, IL; November 12-16, 2016
  • American Society for Cell Biology (ASCB) 2016 Annual Meeting
    San Francisco, CA; December 3-7, 2016

FUTURE CAPABILITIES OF THE GENELAB DATABASE

The GeneLab team is working hard on developing and vetting future capabilities for the public release of the GeneLab Version 2.0 database slated for September 2017. Version 2.0 will feature Google-like, full-text search capabilities and federation to other omics databases including:

DO YOU HAVE A PUBLICATION THAT CITES GENELAB?

We would like to know! Please send us your citation so that we can include it in our metrics and post it on the GeneLab website. genelab-outreach@lists.nasa.gov

Sincerely,
The GeneLab Team

03.16
No. 6: Release of New Datasets by GeneLab

Greetings From GeneLab!

We're happy to share some recent GeneLab highlights with you.

DATA RELEASE

Eight new datasets are now available through the GeneLab Data System. This release includes two datasets that are being released through GeneLab for the first time entitled, "Evaluation of in vitro macrophage differentiation during space flight" (PI: Stephen Chapes), and "RNA-Seq analysis identifies potential modulators of gravity response in Ceratopteris spores: Evidence for modulation by calcium pumps and apyrase activity" (PI: Stanley J. Roux). In addition, six datasets were imported to GeneLab from other databases. This brings the total number of datasets in the GeneLab Data System to 55.  To view the announcement summary page for all the new datasets, please follow this link to the Data Release Announcements. The direct link to the data system is https://genelab-data.ndc.nasa.gov/genelab/.

NASA Space Biology Omnibus NRA:  GeneLab Innovation Awards Research Announcement (ROSBio-2016 Appendix A)

A NASA Research Announcement for Research Opportunities in Space Biology (ROSBio) was released on March 24, 2016. This NRA solicits research that utilizes the GeneLab Data System to translate spaceflight research data into new knowledge relating to the responses of living systems in the spaceflight environment. Non-binding notices of Intents (NOIs) are due April 25, 2016 at 5 PM Eastern Time, and full proposals of 15 pages or less, are due June 28, 2016 at 5 PM Eastern Time. The full-text of the announcement including instructions on how to apply is available through NSPIRES at https://nspires.nasaprs.com/external/solicitations/summary.do?method=init&solId={8CBC2A29-9676-043D-AC8D-ED34AE8D2D88}&path=init.

SpaceX-8 Launch

GeneLab will host omics data from two experiments that are scheduled to launch with the SpaceX-8 resupply mission to the International Space Station on April 8, 2016.

Microbial Tracking-1C (MT-1C) is part three of a three-part investigation that seeks to characterize airborne and surface-associated populations of microorganisms aboard the International Space Station. MT-1A and MT-1B launched on board SpaceX-5 and SpaceX-6 respectively.  All three MT-1 investigations will contribute metagenomic data to GeneLab.

GeneLab will also host transcriptomic, proteomic and epigenomic data from the Influence of Microgravity on the Production of Aspergillus Secondary metabolites or IMPAS experiment (Micro-10). The experiment uses both wild-type and mutant strains of Aspergillus nidulans to determine whether the microgravity environment alters gene expression and thus the production of  metabolites by the fungus. In particular the investigators are interested in the production of secondary metabolites – compounds that provide a selective advantage to fungi but are not essential for growth or reproduction –  that can be exploited by humans to make beneficial pharmaceuticals.

NASA TV coverage of the SpaceX-CRS-8 launch scheduled for Friday, April 8, 2016, at 4:43 p.m. EDT will be available for viewing on: http://www.nasa.gov/multimedia/nasatv/

GeneLab at the 2016 Experimental Biology Conference

GeneLab will attend the Experimental Biology Conference, April 2-6, 2016, at the San Diego Convention Center in San Diego, CA. The Space Biology project office at NASA's Ames Research Center will be co-hosting a booth exhibit with GeneLab at this annual meeting of professional research scientists from fields of study including anatomy, biochemistry, molecular biology, pathology, nutrition, pharmacology, and physiology.

To see photos and details of GeneLab at other events, please use this events link

Sincerely,
The GeneLab Team

02.16
No. 5: New GeneLab Mouse Datasets, Space Biology GeneLab
RFI, 2016 HRP Investigators’ Workshop and more!

Greetings From GeneLab!

We’re happy to share some recent GeneLab highlights with you.

Multi-omic Investigations of Mouse Liver Subjected to Simulated Spaceflight Freezing and Storage Protocols.

We have new datasets available through the GeneLab Data System. To view the announcement summary page for the new release, please follow this link to the Data Release Announcements. The direct link to the new data sets is:
https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-49/

NASA Space Biology Request for Information (RFI) on Reference Omics Experiments for GeneLab Science Definition Team

GeneLab would like to thank all those who contributed to this very important RFI. We know that your time is valuable and your input to the formulation of an omics reference mission is greatly appreciated. We hope that this mission will serve the broadest scientific community possible. We will send updates via future newsletters on the outcome from the RFI and the development of the reference mission.
NASA will establish an internal Science Definition Team (SDT) to use the community inputs provided by respondents to this RFI (and a subsequent workshop) to design one or more reference experiments/investigations.  After the experiment, the raw data will be posted online at the NASA GeneLab data repository website (https://genelab-data.ndc.nasa.gov). 

Solicitation Number: NNH16ZTT001L
Release Date: Nov 05, 2015
Response Date: Feb 05, 2016 CLOSED

GeneLab at the 2016 Human Research Program Investigators' Workshop 

To see our activities at this meeting, please use this events link

Sincerely,
The GeneLab Team

01.16
No. 4: New GeneLab Rodent Datasets, Space Biology
GeneLab RFI, ASCB 2015 Recap

Greetings From GeneLab!

We are writing to inform you that we have new datasets available through the GeneLab Data System. To view the announcement summary page for the new release, please follow this link Data Release Announcements. Direct links to the individual data sets are provided below: 

Omics Analyses of Mouse Liver in Microgravity on the Rodent Research-1 Payload

https://genelab-data.ndc.nasa.gov/genelab/search_studies/?q=RR1

New NASA Space Biology Request for Information (RFI) on Reference ‘Omics Experiments for GeneLab Science Definition Team

Solicitation Number: NNH16ZTT001L
Release Date: Nov 05, 2015
Response Date: Feb 05, 2016

NASA's Space Biology program investigates primary mechanisms behind changes in living systems due to spaceflight and microgravity in hopes of developing the foundations for a human presence in space for extended periods in preparation for exploration.  Another goal is to apply this knowledge and technology to improve our nation's competitiveness, education, and the quality of life on Earth.

NASA seeks inputs to this RFI so that it can design ‘omics reference experiments needed by the Space Life Sciences community. NASA will establish an internal Science Definition Team (SDT) to use the community inputs provided by respondents to this RFI (and a subsequent workshop) to design one or more reference experiments/investigations.  After the experiment, the raw data will be posted online at the NASA GeneLab data repository website (https://genelab-data.ndc.nasa.gov).  It is anticipated that the results will be used to issue open solicitations for proposals from the science community for further bioinformatics analysis.

The full text of the RFI and response instructions can be found at:
http://tinyurl.com/NNH16ZTT001L.
Responses must be submitted electronically using the NSPIRES web site. This RFI is open to responses from all parties including commercial entities, international organizations, academia, NASA Centers, and other government agencies. The information obtained will be used by NASA for planning and acquisition strategy development.

 

NASA will use the information obtained as a result of this RFI on a non-attribution basis.  Providing data and information that is limited or restricted for use by NASA for that purpose would be of very little value and such restricted/limited data/information is not covered under this request.  No information or questions received will be posted to any website or public access location.  NASA does not plan to respond to the individual responses. The Government does not intend to award an award on the basis of this RFI or to otherwise pay for the information solicited. 

In addition to the data releases, GeneLab attended the following meeting. For more information please use this events link

American Society for Cell Biology (ASCB)

GeneLab and Space Biology staffed an exhibit booth at the annual meeting of the American Society for Cell Biology (ASCB), December 12-15, 2015 in San Diego, California. An estimated 9000 attendees participated in a packed schedule over five days. During the three exhibit days over 200 visitors engaged NASA scientists to learn more about the cell biology research NASA supports and hear about the upcoming funding opportunities for the GeneLab Innovation Awards and the Space Biology program. Many new investigators who visited the booth were introduced to GeneLab and encouraged to explore the omics data sets currently available in the data system. Also on hand was a disposable flowpath assembly for demonstrating NASA’s spaceflight cell culture capabilities of the Bioculture System.

Of the visitors to the booth, approximately 50% were junior or senior researchers looking for grant funding opportunities, 30% were post-doctoral candidates seeking fellowship opportunities, 10% were students seeking internships and the final 10% were fellow exhibitors who were for-profit companies seeking information on how to do business with NASA. There was also interest from several senior researchers wanting to learn about accessing space-flown rodent tissues through the Biospecimen Tissue Sharing Program. In addition to the exhibit booth, NASA scientist Dr. Sigrid Reinsch presented a poster on GeneLab titled, “GeneLab: A systems biology platform for spaceflight omics data.” Space Biology Principal Investigators Drs. Elizabeth Blaber and Eduardo Almeida presented their co-authored poster, “CDKN1a/p21 regulates load-dependent stem cell-based osteoprogenitor differentiation into mineralized tissue.” NASA representatives from Ames Research Center who participated in staffing the booth included: Sandy Dueck, Elizabeth Keller, Sigrid Reinsch, Elizabeth Blaber, and Eduardo Almeida. The interest level from the ASCB attendees at the 2015 annual meeting was very high with a number of booth visitors expressing surprise and excitement that NASA engages in, and funds cell biology research.

Dr. Reinsch also participated in a workshop entitled “Foundational Cell Biology: Making BIG Data Accessible for Teaching and Learning.” There were approximately 100 people in attendance at the workshop, mostly college and university professors. Dr. Reinsch briefly presented a synopsis of GeneLab. The participants were very impressed with the open nature of the database, and there was general interest to use the GeneLab datasets for classroom learning. Several participants with systems biology expertise were pleased to hear that there will be future funding for analysis proposals.  

Sandy Dueck participated in a workshop entitled “Simple Social Media for Scientists” to learn tools to promote GeneLab through scientific social media networks.

Sincerely,
The GeneLab Team

12.15
No. 3: ASGSR, AMIA, Picaut, etc

Greetings From GeneLab!

We are writing to inform you that we have new datasets available through the GeneLab Data System. To view the announcement summary page for the four new releases, please follow this link:

GeneLab Data Release Announcements

Direct links to the individual data sets are provided below: 

Comparison of the Spaceflight Transcriptome of Four Commonly Used Arabidopsis thaliana Ecotypes

Microbiomes of the Dust Particles Collected From the International Space Station and Spacecraft Assembly Facilities

Proteomics and Transcriptomics Analysis of Arabidopsis Seedlings in Microgravity

STS-135 Mouse Liver Transcriptomics

In addition to the data releases, GeneLab will be attending the following Fall events. For more information on these events, please follow this link:

GeneLab Events

Bay Area Science Festival STEAM Carnival
GeneLab will be present at the NASA booth at the 2015 Bay Area Science Festival’s STEAM Carnival, November 7, 2015 in San Francisco, CA.

American Society for Gravitational and Space Research (ASGSR)
Come join us at ASGSR on November 10-15, 2015 in Alexandria, VA and find out what's new with GeneLab.

American Medical Informatics Association (AMIA)
Join the GeneLab project at the AMIA Annual Symposium in San Francisco, CA, November 14-18, 2015.

American Society for Cell Biology (ASCB)
Look for the GeneLab project at the NASA Space Biology outreach booth at the ASCB meeting in San Diego, CA, December 12-16, 2015.

Sincerely,
The NASA GeneLab Team

11.15
No. 2: CASIS Survey

Greetings GeneLab Users,

GeneLab would like to call your attention to a CASIS survey currently available to the public, and intended to garner information about the most relevant model organisms for human disease research. 

The Center for the Advancement of Science in Space (CASIS) is a nonprofit organization selected by NASA in 2011 to promote and manage research on the International Space Station (ISS) U.S. National Laboratory. The objective of CASIS (http://www.iss-casis.org/) is to expand utilization of the ISS for scientific research and technology development that will benefit those on Earth.

As part of this mission, CASIS has initiated an effort to utilize research on the ISS to improve human health on Earth - particularly the prevention, identification, and treatment of disease. CASIS has termed this initiative the “Good Health Campaign.” 

We are contacting you to inquire if you would be willing to participate in a survey to share your subject matter expertise and help CASIS shape the initiatives they intend to pursue under the Good Health Campaign. Specifically, we are interested in understanding the most appropriate model organisms, types of samples, and data analysis approaches used in your field to better understand human disease. 

The disease areas of primary interest for initial investigation on the ISS National Lab include the following:

  • • Musculoskeletal defects/disease
  • • Radiation effects, particularly on the nervous system
  • • Microbiome alterations
  • • Cardiovascular deconditioning
  • • Immune dysfunction
  • • Intracranial hypertension
  • • Nutrition and metabolomics
  • • Pharmacology and pharmacokinetics
  • • Cell differentiation and cancer
  • • Aging

The brief survey is found at this web location:
https://www.surveymonkey.com/s/CASIS_GH_Models.
Please direct any questions to Debbie Wells  at CASIS:  dwells@iss-casis.org.
Thank you for your participation.

The GeneLab Team

10.15
No. 1: GeneLab Data System 1.0 Release

NASA is announcing the release of the GeneLab Data System 1.0, the first version of NASA's open-access, online searchable data repository for Space Biology experiments. The GeneLab platform seeks to enhance the use of the International Space Station derived data for development of next generation research. This open access repository for spaceflight data will help to maximize the scientific return from the limited number of biological research opportunities in space. This open access data approach will help to foster innovation and discovery leading to advances for NASA Exploration and Earth-based benefit.


The scientific community is invited to log on to the GeneLab Data System, browse and download data, and to submit new data. Contributions are highly valued and enable the evolution of the data system. Users are also invited to provide feedback, through the Data System, to continually update and improve the capabilities and utility of GeneLab.


This initial 1.0 release of the GeneLab Data System, is part of a larger four-phased development approach to the GeneLab project. This iterative development approach is to enable community feedback and tailored updates to the system. The data system became publicly available on April 15, 2015, and can be found online at:
http://genelab.nasa.gov/data.


More information about GeneLab can also be found in the GeneLab Strategic plan at:
http://genelab.nasa.gov/resources/GeneLabStrategicPlan_Baseline_2014.pdf.

 
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