NASA GeneLab is expected to capture and distribute omics data and experimental and process conditions most relevant to research community in their statistical and theoretical analysis of NASAs omics data

Berrios, Daniel C.

Thompson, Terri G.

NASA Technical Reports Server

GeneLab 
Daniel C. Berrios MD MPH PhD 
Terri G. Thompson PhD 
https://ntrs.nasa.gov/search.jsp?R=20160001751 2019-08-31T04:21:00+00:00Z
Flight Research: International Space Station 
2 
• Almost as soon as the International 
Space Station was habitable, 
researchers began using it to study 
the impact of microgravity and 
other space effects on several 
aspects of our daily lives.  
 
• This unique scientific platform 
continues to enable researchers 
from all over the world to put their 
talents to work on innovative 
experiments that could not be done 
anywhere else.  
2015 NRC CBPSS Cte Mtg 4/1/2015 
GeneLab Strategic Plan 
3 
 
 
“… there is a significant demand from the 
scientific community for NASA-funded 
research opportunities on the ISS that cannot 
be met using traditional management tactics 
based on single Principal Investigator (PI)-led 
investigations. Given the factors that limit the 
scientific output required to address the 
significant biological problems required for 
human exploration beyond low-earth orbit, 
NASA will develop and implement a new multi-
investigator approach based on high content 
bioinformatics analytics and with open science 
and data.” 
-GeneLab Strategic Plan, 2014 
2015 NRC CBPSS Cte Mtg 4/1/2015 
GeneLab Goals 
4 
The GeneLab Goals 
 
1. “Develop an integrated repository and bioinformatics data system for analysis 
and modeling “ 
 
2. “Enable the discovery and validation of molecular networks that are 
influenced by space conditions through ground-based and flight research 
using next-generation omics technologies” 
 
3. “Engage the broadest possible community of researchers, industry, and the 
general public to foster innovation” 
 
4. “Strengthen international partnerships by leveraging existing capabilities and 
data sharing “ 
-GeneLab Strategic Plan, 2014 
 
 
2015 NRC CBPSS Cte Mtg 4/1/2015 
Motivations 
5 
• Maximize ROI for ISS Utilization: Open-access, systems-biology spaceflight 
experiments will provide foundational science that maximizes return-on-investment for 
rare and costly spaceflight opportunities and remove research “bottleneck” 
• Create a PI Multiplier Effect: Open access greatly expands the community of 
researchers using ISS derived data for investigations – ISS research investments will yield 
numerous follow-up investigations and next generation hypothesis-driven research 
• Leverage NASA and External Partner Strengths: Brings together NASA’s strengths 
in Space Biology and “big data” analysis with commercial, government and international  
partners through a scaled and iterative approach that capitalizes on existing databases, 
analytical tools  and biotech capabilities 
• Maximize Utilization of Cutting Edge Bioanalytical Tools and Techniques: 
Multiple omics datasets and integrated data system allows scientists to interrogate ISS 
derived samples using state-of-the-art high throughput genomics, proteomics, 
metabolomics and bioinformatics tools 
• Speed the Pathway to Translation: Allows researchers to discover emergent 
properties in data to identify and understand pathways/macromolecules influenced by 
space stressors 
• Directly responsive to 2011 Decadal Survey Recommendations and OSTP Open Data 
Initiative.   
• Similar goals and efforts NASA ARMD and SMD to increase ROI and PI Multiplier effect 
and engage broad communities.  ARMD/AvS/DashLink, SMD/SS/PDS, SMD/ES/EOS-
EOSDIS & NEExchange.  
2015 NRC CBPSS Cte Mtg 4/1/2015 
ISS Research  
6 
• The unique conditions and 
workflows aboard the ISS are 
captured for a flight experiment 
and associated with the results.  
• This information is ingested, 
stored, indexed and distributed 
from NASA’s Life Science Data 
Archive.  
• NASA GeneLab is expected to 
capture and distribute ‘omics’ 
data and experimental and 
process conditions most 
relevant to research community 
in their statistical and 
theoretical analysis of NASA’s 
omics data. 
NASA astronaut Barry "Butch" Wilmore setting up 
the Rodent Reseach-1 Hardware in the Microgravity 
Science Glovebox aboard the International Space 
Station 
2015 NRC CBPSS Cte Mtg 4/1/2015 
 
 
 
 
Analysis 
Modeling 
Data 
Repository 
Bioinformatics 
System 
Sample 
Processing 
Flight 
Research 
Ground 
Research 
Research 
Initiatives 
Background: GeneLab Vision 
Access to 
Data 
Data 
Generation 
from Model 
Organisms 
Vision: A centralized collaboration space for data deposition, retrieval, 
analysis and modeling to develop next generation science related to 
spaceflight 
7 
2015 NRC CBPSS Cte Mtg 4/1/2015 
GeneLab Organization 
2015 NRC CBPSS Cte Mtg 8 4/1/2015 
GeneLab 
Project Office 
PM – Joe Coughlan 
DPM – Yung Nguyen 
Space Life and Physical Sciences 
NASA HQ 
Nicki Rayl 
 
Data Systems 
 
 Design, planning,  
implementation,  
testing, verification,  
and deployment of 
data systems. 
 
Science & Outreach 
Terri Thompson 
 
Managing, directing,  
and controlling  
of GeneLab science  
investigation aspects. 
ISS Program 
Sharon Conover/JSC  
HQ and SLPS 
ARC 
JSC 
Key: 
Data Architect 
D. Berrios 
Space Biology Project 
PM – Jeff Smith 
 
Payload Planning 
L Timucin 
 
Development and  
execution of GeneLab  
payload plans, timelines,  
schedules and missions 
 
Sample Processing  
& Analysis 
K. Chakravarty 
 
Designing QC on spaceflight  
ground samples, cataloging  
payload samples 
 
Data Processing /Operations 
H. Fogle 
 
Quality assessment,  
processing pipelines,  
analysis, modeling,  
algorithm development 
GeneLab Users 
9 
• Traditional Space Biology PI Community – zoologists, botanists, microbiologists, cellular 
and molecular biologists 
 
• Non-Traditional Genomics and Systems Biology Communities 
 
• NASA Human Research Program Omics Data – GeneLab potential host for One Year 
Twins Study Data – Pilot Study for Human Omics Data. Potential repository for ground 
radiation studies using model organisms 
 
• CASIS – Opportunity for data mining to identify targets for drug development, 
personalized medicine and systems biology of model organisms and humans yielding 
knowledge for terrestrial applications and acceleration of translation pathway 
– CASIS funded investigators encouraged to submit raw data to GeneLab 
 
• CASIS participated in 2013 GeneLab RFI 
• CASIS representation at September 2013 Omics Workshop 
• CASIS representation on continuing GeneLab Steering Committee and planning efforts 
 
 2015 NRC CBPSS Cte Mtg 4/1/2015 
10 
Material sent back to earth for 
processing in investigators lab. 
Controls (ground and/or flight) 
processed at the same time. 
Experiment on ISS 
Extracted DNA, RNA and/or protein 
sent to validated omics center to 
generate sequence, transcript or 
protein expression data. 
Crew performs experimental 
protocol and harvests tissues. 
Process Samples 
Data returned to investigator or 
GeneLab for analysis. Raw data 
uploaded into GeneLab database  
for pubic viewing. 
Wet lab validation and 
computational  modeling.  
Return to Earth 
Data shared with larger scientific 
community. Results feedback to 
GeneLab and other databases  
accelerating scientific discovery by 
leveraging a bigger community.  
Experiment is 
prepared and 
launched 
according to 
approved NRA. 
Data Sharing 
Launch 
Modeling and Validation 
Iterative research solicitations for 
experiments utilizing GeneLab data 
for ground validation and next 
generation flight research. 
Next Generation Research 
Data Collection & Hosting 
Concept of Operations 
2015 NRC CBPSS Cte Mtg 4/1/2015 
11 
Mission Types 
Mission Type Definition Example 
Dedicated Reference Data 
Mission is entirely dedicated to GeneLab  
objectives; the Science Definition Team (SDT) 
 defines the experiment and requirements;  
SDT is selected through the NASA Research 
Announcement Process 
Micro-16 
(tissue TBD) 
Collaborative 
Sample Sharing 
GeneLab obtains specimens/samples from 
the existing PI space flight and ground control 
experiment 
Rodent Research 
(Mouse) 
Bioculture System 
Validation  
(Mouse cells) 
Augmentation 
GeneLab provides supplemental funding to a PI 
experiment to increase the quantity and/or  
type of specimens to obtain dedicated sample; 
augmentation requires NASA SLPS experiment 
review approval process 
BRIC-19 (plant), BRIC-20 
(plant) 
 
(BRIC=Biological 
Research in Canisters) 
2015 NRC CBPSS Cte Mtg 4/1/2015 
12 
Launch – Flight Experiment Selection 
Flight experiment solicitation and selection follows the NASA SLPS 
peer review process. 
• NASA HQ through SLPS Program 
• Space Biology Project Office 
• Follow Decadal Survey recommendations 
• Science Definition Team Solicitation Plan  
 
http://www.nasa.gov/sites/default/files/files/NACRS_SLPSResearch_022414T.pdf 
 
2015 NRC CBPSS Cte Mtg 4/1/2015 
13 
Collaborative Datasets 
Year Payload Mission Type 
2015 BRIC-19 
 
University of 
Wisconsin 
Augmentation, 
plant 
BRIC-20 Ohio 
University 
Augmentation, 
Plant 
RR-1* NASA/CASIS Sample Sharing, 
Rodent  
RR-2* Loma Linda 
University; 
Florida State 
University 
Sample Sharing, 
Rodent 
Bioculture* 
Validation 
NASA Sample Sharing, 
mouse cells 
Micro-9* PI data only 
*Additional work proposed for 2015 current out of scope 
2015 NRC CBPSS Cte Mtg 4/1/2015 
14 
Process Samples 
• Flight and/or ground samples received in Laboratory 
• Researcher extracts DNA, RNA and/or Protein 
• Extracted material sent to center for data generation 
• Data is sent back to researcher from center 
2015 NRC CBPSS Cte Mtg 4/1/2015 
15 
Data returned to investigator or 
GeneLab for analysis. Raw data 
uploaded into GeneLab database  
for pubic viewing. 
Wet lab validation and 
computational  modeling.  
Data shared with larger scientific 
community. Results feedback to 
GeneLab and other databases  
accelerating scientific discovery by 
leveraging a bigger community.  
Data Sharing 
Modeling and Validation 
Iterative research solicitations for 
experiments utilizing GeneLab data 
for ground validation and next 
generation flight research. 
Next Generation Research 
Data Collection & Hosting 
Extracted DNA, RNA and/or protein 
sent to validated omics center to 
generate sequence, transcript or 
protein expression data. 
Process Samples Material sent back to earth for 
processing in investigators lab. 
Controls (ground and/or flight) 
processed at the same time. 
Experiment on ISS 
Crew performs experimental 
protocol and harvests tissues. 
Return to Earth 
Experiment is 
prepared and 
launched 
according to 
approved NRA. 
Launch 
Concept of Operations 
Overview of the flow of  
data through the system 
• Sample to data 
• Data Collection & Hosting 
• Information sharing 
• Reuse of data 
2015 NRC CBPSS Cte Mtg 4/1/2015 
16 
Process Samples 
• Flight and/or ground samples received in Laboratory 
• Researcher extracts DNA, RNA and/or Protein 
• Extracted material sent to center for data generation 
• Data is sent back to researcher from center 
2015 NRC CBPSS Cte Mtg 4/1/2015 
17 
Process Samples – Omics Data 
(from Oltvai-Barabasi, Science, Oct 02) 
"Life's Complexity Pyramid" 
2015 NRC CBPSS Cte Mtg 4/1/2015 
18 
Data Collection and Hosting 
• Flight and/or ground samples are processed to generate Omic data 
• Raw and metadata are assessed for completeness and quality by GeneLab 
personnel 
• Completed data is uploaded into data system 
• Datasets are published in the system and available to the public 
2015 NRC CBPSS Cte Mtg 4/1/2015 
19 
Data Sharing 
• Space biology research data hosted by GeneLab is freely available to all 
• Researchers can download datasets for analysis, modeling, validation 
• Researchers can publish data, methods, results and thoughts 
 
2015 NRC CBPSS Cte Mtg 4/1/2015 
20 
Modeling and Validation 
Wet lab validation and computational modeling 
Biological Network 
2015 NRC CBPSS Cte Mtg 4/1/2015 
21 
Next Generation Research 
Iterative research solicitations for experiments utilizing GeneLab data for ground validation 
and next generation flight research. 
Model  
Validation 
Model Analysis 
Hypothesis  
Generation 
Experiment  
Data  Generation 
Experiment 
Analysis 
Modeling Experimental G
LD
S 
Lab
o
rato
ry 
(G
ro
u
n
d
/Fligh
t) 
Model  
Construction 
Public Data 
Acquisition 
Public Data 
Acquisition 
Biological 
Insight 
Public Data 
Acquisition Public Data 
Acquisition Biological 
Insight 
2015 NRC CBPSS Cte Mtg 4/1/2015 
22 
New Grant Opportunities and Missions 
Model  
Construction 
Model  
Validation 
Model Analysis 
Hypothesis  
Generation 
Experiment   
Data   
Generation 
Experiment 
Analysis 
Modeling Experimental 
Biological Insight 
Biological Insight 
G
LD
S 
Lab
o
rato
ry 
(G
ro
u
n
d
/Fligh
t) 
Experiment is 
prepared and 
launched 
according to 
approved 
NRA. 
Launch 
• Next generation of grant proposal 
• New flight missions 
• Computational modeling  
• New hypothesis  
2015 NRC CBPSS Cte Mtg 4/1/2015 
GeneLab Phased Implementation 
23 
Phased Implementation 2014-2020 
IT Systems 
• Link to Public Databases 
• Beta Space 
Bioinformatics system 
Science 
• Omics Center 
Selection 
• Data analysis from 
initial ground studies 
• Science Definition 
Teams Identified 
• Outreach Program 
Plan 
IT Systems 
• Integrated Platform across 
model organisms 
• Build Community via 
collaborative science 
Science 
• Continue ground controls and 
process enhancement  
• Engage with Scientists 
external to NASA as part of 
Outreach Program 
• Dedicated flight experiments 
         Phase 1 
    Searchable Data 
       FY2014 –2015 
         Phase 2 
      Data Acquisition 
        FY2015-2016 
       Phase 3 
  System Integration  
     FY2017 – 2018 
Phase 4 
 Implementation 
FY2019 – 2020 
IT Systems 
• System Requirements & 
Architecture  
• Public Website 
• Searchable Data Repository 
• Requirements level 1 
Science 
• Omics Center Solicitation 
• Protocol Development 
• Data analysis validation 
• Initiate ground controls 
Collaborate with two 
manifested flight experiments 
• SDT Solicitation for Dedicated 
Flight 
 
 
Full 
Implementation 
Begin 
Implementation 
• Full science community 
engagement 
• Development of analytical and 
Modeling tools  
• Ongoing dedicated flight 
experiments 
• Website and platform 
sustaining activities 
• Continuous improvement 
2015 NRC CBPSS Cte Mtg 4/1/2015 
Salient Questions / Science 
• How should the current state of analytics for 
proteomics and metabolomics influence 
choice of global profiling design vs. more 
focused experiments?  
• How to use resources wisely to generate 
longitudinal datasets and support experiment 
(organism/tissue/assay) diversity? 
 
 
 
 
 
 
2015 NRC CBPSS Cte Mtg 24 4/1/2015 
Salient Questions / Data Systems 
• What is the value of providing biocomputing 
capabilities in terms of increasing scientific 
throughput?  
– Access to high performance computing resources 
– Biocomputing tools repository 
– Is there analogy to collaborating teams of 
scientists in Earth Science 
 
 
 
 
 
2015 NRC CBPSS Cte Mtg 25 4/1/2015 
Salient Questions / Science 
• What are the data boundaries of scientific 
relevance vis-a-vis the environment of 
spaceflight experiments? 
– 60K+ ISS parameters 
– Selections by PIs may overlook parameters 
– Data archived approx. every 2 years, after which 
retrieval is much more difficult 
 
 
 
 
 
2015 NRC CBPSS Cte Mtg 26 4/1/2015 
Salient Questions / Science 
• How can the SDT maximize relevance of flight 
experiment data to ground-based 
experiments? 
• How can we expand the user-base of the flight 
experiment data to include more researchers 
performing ground-based experimentation? 
 
 
 
 
 
2015 NRC CBPSS Cte Mtg 27 4/1/2015 
Salient Questions / Data Systems 
• How can GeneLab best support biological 
model development, analysis, validation? Best 
leverage distributed scientific knowledge? 
– Data Discovery/Federation  
– Data annotation/Knowledge Capture 
– Data visualization 
– Develop in-house capabilities 
– Integrate externally-developed capabilities 
– Direct users to external systems and tools  
 
 
 
 
 
2015 NRC CBPSS Cte Mtg 28 4/1/2015 
Salient Questions / Data Systems 
• How best to represent Omics metadata?  
– Myriad, rapidly evolving metadata standards  
– Newer Omics data types have no metadata 
standards yet 
• Data formats 
• metadata, protocols and analyses 
– How to capture the unique aspects of space 
biology experiments as metadata and related 
data?  
 
 
 
2015 NRC CBPSS Cte Mtg 29 4/1/2015 
GeneLab Staff 
30 
Project Manager – Joe Coughlan 
Deputy Project Manager – Yung Nguyen 
Project Scientist –  Terri Thompson 
Outreach Lead – Jon Rask 
Payload Lead – Linda Timucin 
Data Systems Lead/Architect – Daniel Berrios  
Lead Developer – Chris Middour 
Database System/Web Engineer – Jon Welch 
Bioinformatics Scientist – Homer Fogle 
Ground Lab Science R&D Lead – Kaushik Chakravarty 
Lab Manager – Sam San-Huei Lan 
Lab Technician – Rick Chen 
Project Analyst/Configuration Manager – Nikita Gilkerson 
Project Coordinator – Desireemoi Bridges 
 
31 
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2015 NRC CBPSS Cte Mtg 4/1/2015 


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