Signature Common LINCS Hackathon Session

[raynamharris]

Millions of transcriptomics samples were generated by the Library of Integrated Network-Based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus, connections between drugs, genes, pathways, and diseases can be illuminated. SigCom LINCS is a web-based search engine that serves over 1.5 million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built from the Signature Commons framework, a cloud-agnostic generic platform that can be used to stand up Data Commons with a focus on searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up- and down-genes. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures, and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) compliant with metadata linked to standard ontologies and vocabularies while all data and signatures within SigCom LINCS are available for download and via a well-documented API. In summary, SigCom LINCS has the potential to accelerate drug and target discovery in systems pharmacology.

[AviMaayan]

Hi @raynamharris can you please update the description to the following:

Millions of transcriptomics samples were generated by the Library of Integrated Network-Based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus, connections between drugs, genes, pathways, and diseases can be illuminated. SigCom LINCS is a web-based search engine that serves over 1.5 million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built from the Signature Commons framework, a cloud-agnostic generic platform that can be used to stand up Data Commons with a focus on searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up- and down-genes. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures, and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) compliant with metadata linked to standard ontologies and vocabularies while all data and signatures within SigCom LINCS are available for download and via a well-documented API. In summary, SigCom LINCS has the potential to accelerate drug and target discovery in systems pharmacology.

[AviMaayan]

The SigCom LINCS session will have two 45 minute interactive presentations followed by a general discussion. The first interactive presentation will cover programmatic access to SigCom LINCS by the SigCom LINCS developer John Erol Evangelista. The second interactive presentation will demonstrate how to build Appyters and how to use the SigCom LINCS APIs within Appyters. The presentation about Appyters will be given by Daniel Clarke who developed the Appyters system.

Agenda: 3:00 - 3:45 ET SigCom LINCS APIs - John Erol Evangelista, LINCS-DCIC, Ma'ayan Lab, Icahn School of Medicine at Mount Sinai, New York, NY 4:00 - 4:45 ET Introduction to building Appyters - Daniel Clarke, LINCS-DCIC, Ma'ayan Lab, Icahn School of Medicine at Mount Sinai, New York, NY

[jessicalumian]

Here is the Jupyter Notebook from the first presentation: https://github.com/MaayanLab/sigcom-lincs/blob/main/tutorials/API%20Access/Hackaton%20Demo.ipynb