GeneLab Analysis Working Groups

January 5, 2018 –

GeneLab is recruiting members for Analysis Working Groups to analyze NASA omics data!

NASA’s GeneLab Project is recruiting investigators, bioinformaticians, graduate students, and postdocs to participate in Analysis Working Groups (AWGs) that will investigate specific subsets of omics data from experiments conducted onboard the International Space Station, the Space Shuttle, as well as ground-based research with relevance to spaceflight (e.g. radiation or unloading/weightlessness)

GeneLab is a science collaboration initiative and data system effort that provides a workspace with tools to analyze and visualize omics data. GeneLab has established AWGs with the goal of maximizing the generation of new knowledge from these rare and complex spaceflight datasets.

The project has established five different AWGs – scientific groups of excellence focused on analyzing spaceflight relevant omics data within the GeneLab Data System (GLDS). Below is a list of the groups and their leads:

The primary activity of each AWG will be to establish analytical processes to generate higher-order data from data in the GLDS with relevance to one or more specific application areas. For example, the mammalian AWG will analyze all data relevant to mammalian systems (human, mouse, rat, etc.). The multi-omics group will focus on gaining new knowledge using systems biology approaches: e.g. how do transcriptomics and proteomics compare within the same dataset? What are the common molecular signals induced by spaceflight across the various species?

The AWG participants will help assess and improve the effectiveness of GeneLab through intensive utilization of data analysis tools. These investigations are anticipated to lead to one or more scientific publications, as well as implementation of specific data visualization strategies to disseminate new knowledge from these analyses.

A kick-off meeting for the AWG will be held January 25, 2018 at the Human Research Program Investigators’ Annual Workshop in Galveston, TX, and virtually. Members from all five AWGs will meet in this first session. Each AWG will then meet separately in monthly teleconferences to become familiar with datasets and tools in the GLDS, and to provide initial feedback on how to gain new knowledge from the data. All AWGs will meet in-person for a two-day workshop in April 2018 to finalize the establishment of processing pipelines. The GLDS data processing will take place during the summer of 2018 with GeneLab hosting 10 student interns at NASA Ames Research Center. Students will be encouraged to submit their most significant findings to the annual meeting of the American Society for Gravitation and Space Research, October 31 – November 3, 2018, and to join the conference to support training sessions for the introduction of the GeneLab toolshed. We anticipate the most exciting results to also be submitted for publication.

If you are interested in participating, and/or if you have students with strong bioinformatics skills who might also be interested in joining, please review the GeneLab Analysis Working Groups Charter and contact the lead of the group you would like to join (see list above). Interested scientists having the required specialized capabilities/qualifications to support the work described in AWG charter are asked to submit a capability/qualification statement. There is no required font size and/or type designated for this Capability/Qualification Statement. Submit your response electronically in PDF format. The response must include the following: 1) Contact: name, affiliation, address, phone, e-mail, and website (if applicable). 2) Subject area expertise. Please provide a concise description of your expertise in terms of omics analyses including a list of relevant work and publications performed in the past five (5) years. Access to the AWG will be on a first come, first served basis (currently at 75% capacity).

Looking forward to hearing from you!



GeneLab Analysis Working Groups Charter

Purpose

The purpose of the GeneLab Analysis Working Groups (AWGs) is to optimize the processing of raw omics data from the GeneLab repository in order to maximize the gain of new knowledge from such complex datasets. The AWGs will also assess and improve the effectiveness of the GeneLab Data System (GLDS) through intensive utilization of the analytics to be deployed therein.

Organization and Function

The AWGs aspire to scientific excellence, and participation in AWGs is strictly on a volunteer basis. The primary activity of each AWG is to establish analytical processes to generate higher order data from data housed in the GLDS with relevance to one or more specific application areas. For example, a mammalian AWG would analyze all data relevant to mammalian systems (human, mouse, rat, etc.). The GeneLab AWGs aspire to yield:

  1. Canonical data analysis pipelines. The interpretation of analysis results is too often confounded by variability in data-processing protocols. This can make comparison of results between studies even more difficult. By developing canonical analysis pipelines, the AWGs will help speed the harmonization of results across space biology experiments.
  2. Processed (“higher-order”) space biology data. The AWGs will work with GeneLab staff to generate processed data using the canonical analysis pipelines. This higher-order data will be made available to the broader scientific community through the GLDS. This data will serve as a reference to the community on use of the pipelines, and will be fully reproducible using the GLDS and referenced pipelines. Optimal strategies regarding the display of processed data to the scientific community will also be discussed.
  3. Critiques of the GLDS. The value of the GLDS to the scientific community is best judged through extensive use of the systems. As the AWGs will be using the GLDS intensively (see 1 and 2 above), they will be poised to give valuable feedback to GeneLab on its strengths and weaknesses.
  4. Scientific communication of available analyses and interpretations. The AWGs are expected to communicate the development and application of the canonical data analysis pipelines with the broader scientific community. Such communications could take the form of self-published white papers, newsletters, or peer-review publications and conference presentations. These communications will also serve to catalyze the generation of new hypotheses for further experimentation.

Precisely how each AWG reaches these goals will be determined by the AWGs themselves, but, in general, AWGs should hold frequent in-person or virtual meetings to organize work and review progress. The schedule for delivering the above products is set by the Chair in consultation with GeneLab and the other AWG participants.

Participation

The constitution of each AWG must meet the following criteria: (1) have at least one participant who possesses application area expertise; (2) have at least one participant who possesses bioinformatics expertise; (3) have at least one representative from GeneLab. AWG participants are chosen based on a candidate’s ability to provide the scientific or data analysis insight necessary to achieve the AWG goals. AWG participation is entirely voluntary and participants will not be compensated.

Chairs - All AWGs will have a chair (or co-chairs) selected by GeneLab, with input from the scientific community and/or participants of the AWG. Chairs will lead the AWGs and will draft a schedule and review progress of each AWG towards achieving their goals. Chairs will serve for the life of the AWGs, unless they decide to step down, at which time GeneLab or the remaining participants of the AWG will appoint a new Chair.

GeneLab Representative - Each AWG will have a designated representative from GeneLab to help ensure outcomes of the work meet GeneLab criteria and to otherwise support the work of the AWG. A GeneLab representative can also be chair of an AWG.

Coordinators – The following Coordinators will be selected on a volunteer basis by each AWG. Multiple coordinating functions may be performed by a single Coordinator.

  • Analysis Coordinator - The analysis coordinator tracks the progress of individual analyses, ensuring that analyses are done in a consistent and reproducible manner, sets deadlines for completion of individual analyses, and collects and organizes interim and final analysis results.
  • Communication Coordinator – Assembles information for newsletter or manuscript sections, ensures consistency in writing and figure styles, and sets goals for the completion of articles or newsletter.

Expectations for AWG Participation

Participation in GeneLab AWGs is open to all investigators (academic, government, private sector); however participants must be willing to:

  1. Contribute significantly to the goals of the AWG.
  2. Take part in group activities including periodic teleconferences. Participants are expected to actively contribute to the group goals (see above).
  3. Share AWG products with other AWG participants via the collaborative workspace provided by the GLDS.

An investigator that would like to take part in any AWG(s) should provide a description of their expertise in the relevant area of analysis to GeneLab, and must sign a statement of acknowledgement of the Expectations for AWG Participation (see above). Requests for participation in AWGs will be reviewed by GeneLab and the AWG chairs who must reach a consensus to allow the applicant to participate. The AWG chair(s) and GeneLab will review participation in each group yearly.

Benefits of AWG Participation

By participating within a GeneLab AWG, investigators will join a group of scientific excellence and may co-author a landmark paper. They will help set data and analysis standards for the community, and may develop relationships that could lead to additional collaborations.