Synapse
Synapse is a collaborative research platform that allows individuals and teams to share, track, and discuss their data and analysis in projects. Synapse allows researchers to share and describe data, analyses, and other content. Data and analyses can be stored in many types of locations, including private servers, local hard drives, or cloud storage. Synapse provides a common interface to describe these data or analyses, where they come from, and how to use them. Synapse also provides mechanisms for adding and retrieving data, analyses, and their respective descriptions.
Description
More detailed information about this field from each metasource.
Synapse is a collaborative research platform that allows individuals and teams to share, track, and discuss their data and analysis in projects. Synapse allows researchers to share and describe data, analyses, and other content. Data and analyses can be stored in many types of locations, including private servers, local hard drives, or cloud storage. Synapse provides a common interface to describe these data or analyses, where they come from, and how to use them. Synapse also provides mechanisms for adding and retrieving data, analyses, and their respective descriptions.
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Synapse is an open source software platform that clinical and biological data scientists can use to carry out, track, and communicate their research in real time. Synapse enables co-location of scientific content (data, code, results) and narrative descriptions of that work.
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
Webpage:
https://www.synapse.org/Webpage
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https://www.synapse.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://www.synapse.org
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
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Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
other
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
Licence URL
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https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://docs.synapse.org/articles/governance.html
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
Publications:
Publications
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Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
PMID: 24071850
metasource: Fairsharing.org
version: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
PMID: 24071850
metasource: Fairsharing.org
version: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
PubMed citations: 59.
59 articles citing: Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
Identification of the Putative Tumor Suppressor Characteristics of FAM107A via Pan-Cancer Analysis. PMID:35669436
Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations. PMID:35637462
Pan-Cancer Analysis of the N6-Methyladenosine Eraser FTO as a Potential Prognostic and Immunological Biomarker. PMID:34744452
Crowdsourced mapping of unexplored target space of kinase inhibitors. PMID:34083538
NKX6-1 mediates cancer stem-like properties and regulates sonic hedgehog signaling in leiomyosarcoma. PMID:33906647
Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers. PMID:33477536
Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction. PMID:32638010
Engaging a community to enable disease-centric data sharing with the NF Data Portal. PMID:31836719
Annot: a Django-based sample, reagent, and experiment metadata tracking system. PMID:31675914
A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. PMID:31302153
An integrative sparse boosting analysis of cancer genomic commonality and difference. PMID:31282286
Bayesian Hierarchical Varying-sparsity Regression Models with Application to Cancer Proteogenomics. PMID:31178611
Exploring drivers of gene expression in the Cancer Genome Atlas. PMID:30561551
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis. PMID:30030151
AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research. PMID:29973745
GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis. PMID:29931238
Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. PMID:29799486
Reconstruction of kidney renal clear cell carcinoma evolution across pathological stages. PMID:29463849
Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease. PMID:29218889
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. PMID:29186302
A high-throughput molecular data resource for cutaneous neurofibromas. PMID:28398289
The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. PMID:28380360
Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. PMID:28350385
Competing endogenous RNA network analysis identifies critical genes among the different breast cancer subtypes. PMID:28052038
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. PMID:27982081
Systems Approaches to Cancer Biology. PMID:27864348
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Use of big data in drug development for precision medicine. PMID:27430024
Crowdsourcing biomedical research: leveraging communities as innovation engines. PMID:27418159
Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. PMID:27293150
Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types. PMID:27147563
An informatics research agenda to support precision medicine: seven key areas. PMID:27107452
Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin. PMID:26990976
Survival kinase genes present prognostic significance in glioblastoma. PMID:26956052
The mPower study, Parkinson disease mobile data collected using ResearchKit. PMID:26938265
Taking Bioinformatics to Systems Medicine. PMID:26677177
Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA, DNA Methylation, microRNA, and mRNA across Five Human Cancers. PMID:26606135
The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers. PMID:26439496
Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. PMID:26372948
Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer. PMID:26305674
The mRNA related ceRNA-ceRNA landscape and significance across 20 major cancer types. PMID:26304537
Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. PMID:26110843
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. PMID:25984700
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. PMID:25956356
Toward predicting metastatic progression of melanoma based on gene expression data. PMID:25847062
Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. PMID:25832647
Traits and types of health data repositories. PMID:25825668
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. PMID:25691825
Collaboration for rare disease drug discovery research. PMID:25685324
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. PMID:25594743
Toward better benchmarking: challenge-based methods assessment in cancer genomics. PMID:25314947
RTCGAToolbox: a new tool for exporting TCGA Firehose data. PMID:25181531
Toward a systematic understanding of cancers: a survey of the pan-cancer study. PMID:25071824
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. PMID:24999802
Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers. PMID:24874835
Refining gold from existing data. PMID:24625777
Collection, integration and analysis of cancer genomic profiles: from data to insight. PMID:24584084
Credit for code. PMID:24370738
Tags:
Tags
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data storage
metasource: Fairsharing.org
version: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protocol
metasource: Fairsharing.org
version: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
amp-ad knowledge portal
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
dream challenges
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
github
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
nf data portal
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
tcga pan-cancer working group
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
biomedicine
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
query structured data
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
record provenance
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
research communities
metasource: re3data.org
version: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
data storage
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
experimental measurement
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protocol
metasource: Fairsharing.orgversion: FAIRsharing.org: Synapse; Synapse; DOI: https://doi.org/10.25504/FAIRsharing.dnxzmk; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
amp-ad knowledge portal
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
dream challenges
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
github
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
nf data portal
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
tcga pan-cancer working group
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
biomedicine
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
query structured data
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
record provenance
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
research communities
metasource: re3data.orgversion: re3data.org: Synapse; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3B934 last accessed: 2022-11-04
data storage experimental measurement protocol amp-ad knowledge portal dream challenges github nf data portal tcga pan-cancer working group biomedicine query structured data record provenance research communities
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