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The Open Science Download
Summer 2023
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It's been a while since our last newsletter, but a lot has happened. Come check out the latest in Open Science since the start of the new year! |
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AWG Symposium 2023
Open Science hosted the 2023 AWG Symposium – The Year of Open Science. This virtual event allowed the pubic an opportunity to view some exciting open science stemming from the AWG community and was attended by 249 participants. Watch the recording of the event.
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GeneLab Enabled Publications | |
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Batch Effect Correction
Sanders L M, Chok H, Samson F, Acuna A U, Polo S H L, Boyko V, Chen Y C, et al (2022). Batch effect correction methods for NASA GeneLab transcriptomic datasets, Frontiers in Astronomy and Space Sciences.
doi: 10.3389/fspas.2023.1200132
Datasets: OSD-47, OSD-48, OSD-137, OSD-168, OSD-173, OSD-242, OSD-245
Read more.
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Muscle Dysregulation and Aging in Clock-Dependent
Malhan D, Yalçin M, Schoenrock B, Blottner D, and Relógio A, (2023). Skeletal muscle gene expression dysregulation in long-term spaceflights and aging is clock-dependent, npj Microgravity.
doi.org/10.1038/s41526-023-00273-4
Datasets: OSD-99, OSD-101, OSD-103, OSD-104, OSD-105, OSD-370
Continue reading...
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Large Maf TF Family is a Major Regulator of Myofiber Determination
Sadaki S, Fujita R, Hayashi T, Nakamura A, Okamura Y, Fuseya S, Hamada M, et al, (2023). Large Maf transcription factor family is a major regulator of fast type IIb myofiber determination, Cell Reports.
doi.org/10.1016/j.celrep.2023.112289
Dataset: OSD-104
Read more.
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Meta-analysis of Spaceflight Response of Plant Transcriptome
Barker R, Kruse C P S, Johnson C, Saravia-Butler A, Fogle H, Chang H S, Trane R M, et al (2023). Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome, npj Microgravity.
doi.org/10.1038/s41526-023-00247-6
Dataset: OSD-7, OSD-17, OSD-37, OSD-38, OSD-44, OSD-46, OSD-120, OSD-121, OSD-136, OSD-147, OSD-205, OSD-208, OSD-213, OSD-218, OSD-251
Continue reading...
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Novel Monitoring Approach for Space Effects on Astronauts
Sakharkar A and Yang J, (2023). Designing a novel monitoring approach for the effects of space travel on astronauts’ health, Life.
doi.org/10.3390/life13020576
Dataset: OSD-174
Read more.
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Transcriptomic Signature of Worms Exposed to Simulated Microgravity vs Spaceflight
Çelen I, Jayasinghe A, Doh J H, and Sabanayagam C R, (2023). Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans and Comparison to Spaceflight Experiments, Cells.
doi.org/10.3390/cells12020270
Dataset: OSD-41, OSD-42, OSD-112, OSD-113
Continue reading...
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Effects of Zebrafish Liver Exposed to Low-dose Radiation
Cahill T, da Silveira W A, Renaud L, Wang H, Williamson T, Chung D, Chan S, et al, (2023). Investigating the effects of chronic low-dose radiation exposure in the liver of a hypothermic zebrafish model, Scientific Reports.
doi.org/10.1038/s41598-022-26976-4
Dataset: OSD-47
Read more.
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Acinetobacter pitii Adapts to the ISS
Tierney B T, Singh N K, Simpson A C, Hujer A M, Bonomo R A, Mason C E, and Venkateswaran K, (2022). Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station, Microbiome.
doi.org/10.1186/s40168-022-01358-0
Datasets: OSD-252
Continue reading...
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GeneLab Analysis Platform (Galaxy) will be decommissioned on SEPTEMBER 1st, 2023.
On September 1st, 2023, the GeneLab Galaxy platform will be decommissioned. Accounts and data from this server will NOT be saved, and all data associated with all accounts on this server will be purged.
If you wish to save any of your existing histories or data to the new server, please export these data prior to September 1st, 2023, so that you may then import them yourself to the public galaxy server. See https://galaxyproject.org/support/download-data/ for instructions on how to download Galaxy data.
Over the years, the GeneLab Galaxy Platform has served as tool for students to learn bioinformatics analysis and researchers to analyze their omics data and public GLDS datasets. The GeneLab Project thanks the scientific community for utilizing this platform to make discoveries and advance space biology.
If you have any questions, please reach out to arc-dl-osdr-help@mail.nasa.gov.
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ISGP Meeting 2023
The 42nd Annual International Society for Gravitational Physiology (ISGP) meeting took place July 2-7, 2023 in Antwerp, Belgium. The conference focused on physiological phenomena from altered gravitational environment and space travel. On July 4, Dr. Sylvain Costes presented on “Open Science for Life in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery”. His talk covered various aspects of Open Science in space biosciences at NASA, including the Open Science Data Repository, GeneLab, the Ames Life Sciences Data Archive, data curation and reuse, and the Analysis Working Groups.
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Open Science at HRP IWS 2023
On February 7-9, five Open Science members from GeneLab, ALSDA, and NBISC attended the Human Research Program Investigator's Workshop 2023 to give 3 oral and 4 poster presentations. Check out the topics discussed.
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Latest GeneLab Chats
Check out the latest releases of GeneLab Chats on our YouTube channel!
Vidya Manian - AI Drug Repurposing for Muscle Atrophy
Jamaji Nwanaji-Enwerem - Relationship of GCR and Epigentic Clocks in Human Cells
Vidya Manian - Target Genes to Repurpose Drugs for Muscle Atrophy
Pedro Madrigal - Machine Learning to Characterize Antimicrobial Resistance on the ISS
Vidya Manian - DNA Damage Response of Arabidopsis to Spaceflight Stressors
Stefania Giacomello - Considerations for Single Cell and SR Transcriptomics Sample Collection
Geraldine Vitry - Metabolic Crosstalk in Mouse Liver and Muscle
Chris Mason - Microbes Adapting to the ISS
Willain da Silviera
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Meet the Open Science Summer Students 2023
This summer, Open Science accepted eight summer students—James Rohde, Noah Allen, Joanne Thomson, Nova Butte, Tasneem Nora Khokhar, Justin Davis, Vishnu Prasad, and Harlan Phillips—to work with seven mentors, Xavier-Lewis Palmer, Lauren Sanders, Sam Gebre, Danielle Lopez, Lovorka Degoricija, Ana Uriarte-Acuna, and Sigrid Reinsch. The summer students will be working on a variety of tasks inclduing standardizing metadata from bioimaging file formats, processing spaceflight datasets as input to the SPOKE biomedical knowledge graph, identifying patterns in microbial response to changes in environmental CO2, creating a metadata visualization dashboard to capture an overview of the studies within the OSDR, working in Science Communications to help expand OSDR’s social media presence, working on documenting a user manual for the visualization portal and the new multi-study visualization feature, and converting analog metadata for 50,000 tissue samples from mice exposed to simulated Galactic Cosmic Radiation into the Laboratory Information Management System (SLIMS) as well as developing python scripts to automate the data entry task which currently takes multiple manual entry tasks.
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GeneLab Members Expand GL4U to Teach AmpliSeq Bootcamp
The GL4U training program provides undergraduate and graduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data. Continue reading to learn more about the AmpliSeq bootcamp.
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Meet the Expert - Student Edition
On July 24th, Open Science hosted a "Meet the Expert" event for summer students working at NASA Ames and with the AWG community. In this virtual event, four panelists—Chris Sembroski, Parag Vaishampayan, Amber Paul, and Luis Zea—discussed their career paths ranging from industry, to government, and academia. Overall, 51 participants joined the event ranging from high school to graduate students form four different countries. This event was structured such that each panelist had 10 min to discuss their career paths ending with a 20 min Q+A section. This was followed by a social/networking hour immediately after the event on Kumospace, where 27 students connected with the speakers and continued the conversation.
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Open Science at ASGSR 2023
Registration is now open for the ASGSR 2023 conference November 14-18. Keep a look out for presentations by the Open Science team.
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In 2023, a total of 15 transcriptomic, 4 genomic, and 2 proteomic/metabolomic, GeneLab datasets have been added to the Open Science Data Repository this year alone.
To ensure omics data hosted on the GeneLab Data Repository are accessible to and interpretable by a broad scientific audience GeneLab collaborated with our AWG scientific community to develop and standardize consensus processing pipelines for each omics data type. Standardizing pipelines is necessary to minimize variation in data processing, which enables the integration of data from the diverse array of spaceflight and analog experiments hosted on GeneLab. View the latest 26 processed datasets.
Since January, 21 ALSDA (pheno-physiological-behavioral-imaging) datasets have been released. A sampling of these datasets include: behavioral video from drosophila aboard the International Space Station; immunostaining microscopy of the retinal-blood barrier from RR9; muscle calcium uptake data from spectrofluorometry RR1 and RR9; and echocardiogram-ultrasound data from mice exposed to low-dose oxygen ions and protons. These first-to-be-released pheno-physio datasets enable multi-hierarchical analytics between the molecular genomic level to the tissue, organ, system, and whole organismal behavioral levels. Sincerest appreciation to the 100+ ALSDA AWG members who provided feedback on assay metadata and tabular/imaging data standards enabling scientific.
This brings the grand total to 446 datasets in the repository!
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Stay tuned for more exciting news from Open Science in the Fall 2023 newsletter!
The Open Science Team
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