CFDE Information Portal

Library of Integrated Network-based Cellular Signatures (LINCS)

The Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program developed a library that catalogs changes that occur when different types of cells are exposed to a variety of agents that disrupt normal cellular functions, called “perturbagens.” This library integrated data across cell types, perturbagens, and measurements of cellular responses for use by scientists to design and conduct experiments that can help us better understand normal and diseased cellular states and how to alter them. (Retrieved from the NIH Common Fund site)

TRAINING & OUTREACH

Summer Research Program in Biomedical Big Data Science

The LINCS DCC Summer Research Training Program in Biomedical Big Data Science is a research intensive ten-week training program for undergraduates interested in bioinformatics. Summer fellows training in the Ma’ayan Lab at the Icahn School of Medicine at Mount Sinai conduct faculty-mentored research in the areas: data harmonization, machine learning, cloud computing, and dynamic data visualization.

Application deadline: February 1, 2025

LINCS Summer Trainees Virtual Symposium 2024

This virtual symposium hosted by the Ma’ayan Lab and the Mount Sinai Center for Bioinformatics featured the accomplishments of 10 summer trainees during a 10-week research-intensive full-time training program. The projects covered topics such as data integration, data visualization, LLM integration, and knowledge graphs in the field of biomedical data science and bioinformatics, leveraging the power of AI and other computational tools and methods.

Starts: August 8, 2024

Landmark Publication

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. 2018. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell systems. 6. 13-24

Metadata and Processed Data Files

C2M2

1 Current File(s) | 10 Archived File(s)

1 Current File(s)

10 Archived File(s)

Modified 9/18/2023

Current

Filename:
datapackage.zip
Creator: LINCS
Filesize: 169.2 Mb
Date Modified: 9/18/2023
DCC Approved:
DRC Approved:

Archived

Filename:
datapackage.zip
Creator: LINCS
Filesize: 166.0 Mb
Date Modified: 6/15/2023
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 166.7 Mb
Date Modified: 3/21/2023
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 166.2 Mb
Date Modified: 12/2/2022
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 165.5 Mb
Date Modified: 9/14/2022
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 164.2 Mb
Date Modified: 6/20/2022
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 171.1 Mb
Date Modified: 4/14/2022
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 171.1 Mb
Date Modified: 1/11/2022
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 131.1 Mb
Date Modified: 9/29/2021
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 141.3 Mb
Date Modified: 6/2/2021
DCC Approved:
DRC Approved:

Filename:
datapackage.zip
Creator: LINCS
Filesize: 28.1 Mb
Date Modified: 3/24/2021
DCC Approved:
DRC Approved:

XMT

6 Current File(s) | 4 Archived File(s)

6 Current File(s)

4 Archived File(s)

Modified 12/19/2024

Current

Filename:
rummageo_gene_perturbations.gmt
Creator: LINCS
Filesize: 25.6 Mb
Date Modified: 12/19/2024
DCC Approved:
DRC Approved:

Filename:
rummageo_chemical_perturbations.gmt
Creator: LINCS
Filesize: 31.0 Mb
Date Modified: 12/19/2024
DCC Approved:
DRC Approved:

Filename:
l1000_cp.gmt
Creator: LINCS
Filesize: 2.1 Gb
Date Modified: 12/11/2024
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Consensus_Median_Signatures.gmt
Creator: LINCS
Filesize: 19.9 Mb
Date Modified: 9/14/2024
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_CRISPR_KO_Consensus_Sigs.gmt
Creator: LINCS
Filesize: 14.9 Mb
Date Modified: 12/13/2022
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Chem_Pert_Consensus_Sigs.gmt
Creator: LINCS
Filesize: 15.6 Mb
Date Modified: 12/13/2022
DCC Approved:
DRC Approved:

Archived

Filename:
LINCS_L1000_Ligand_Perturbations_up.gmt
Creator: LINCS
Filesize: 87.4 Kb
Date Modified: 6/6/2022
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Chem_Pert_up.gmt
Creator: LINCS
Filesize: 15.5 Mb
Date Modified: 6/6/2022
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Ligand_Perturbations_down.gmt
Creator: LINCS
Filesize: 93.0 Kb
Date Modified: 6/6/2022
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Chem_Pert_down.gmt
Creator: LINCS
Filesize: 13.4 Mb
Date Modified: 6/6/2022
DCC Approved:
DRC Approved:

Attribute Tables

4 Current File(s) | 0 Archived File(s)

4 Current File(s)

0 Archived File(s)

Modified 3/29/2024

Current

Filename:
LINCS_L1000_CRISPR_KO_Perturbation_Consensus_CD_Sigs.h5
Creator: LINCS
Filesize: 317.5 Mb
Date Modified: 3/29/2024
DCC Approved:
DRC Approved:

Filename:
LINCS_L1000_Chemical_Perturbation_Consensus_CD_Sigs.h5
Creator: LINCS
Filesize: 1.4 Gb
Date Modified: 3/28/2024
DCC Approved:
DRC Approved:

Filename:
LINCS L1000 Chemical Perturbations
Creator: LINCS
Filesize: 33.6 Gb
Date Modified: 6/23/2021
DCC Approved:
DRC Approved:

Filename:
LINCS L1000 CRISPR Perturbations
Creator: LINCS
Filesize: 6.5 Gb
Date Modified: 6/23/2021
DCC Approved:
DRC Approved:

Archived

None Available

Knowledge Graph Assertions

1 Current File(s) | 1 Archived File(s)

1 Current File(s)

1 Archived File(s)

Modified 5/8/2024

Current

Filename:
LINCS.zip
Creator: LINCS
Filesize: 11.6 Mb
Date Modified: 5/8/2024
DCC Approved:
DRC Approved:

Archived

Filename:
LINCS.edges.csv
Creator: LINCS
Filesize: 54.6 Mb
Date Modified: 10/26/2023
DCC Approved:
DRC Approved:

Interoperability Assets

ETL Scripts

1 Current File(s) | 2 Archived File(s)

1 Current File(s)

2 Archived File(s)

Modified 11/23/2024

Current

Name:
LINCS_C2M2_Metadata_ETL_Scripts
Creator: LINCS
Date Modified: 11/23/2024
DCC Approved:
DRC Approved:

Archived

Name:
build_file_lincs2021.py
Creator: LINCS
Date Modified: 6/23/2021
DCC Approved:
DRC Approved:

Name:
process_mcf10a_c2m2.py
Creator: LINCS
Date Modified: 5/22/2022
DCC Approved:
DRC Approved:

API Specifications

7 Current File(s) | 1 Archived File(s)

7 Current File(s)

1 Archived File(s)

Modified 1/31/2023

Current

Name:
Enrichr (SmartAPI)
Creator: LINCS
Date Modified: 1/31/2023
DCC Approved:
DRC Approved:

Name:
FAIRshake API v2 (SmartAPI)
Creator: LINCS
Date Modified: 4/5/2022
DCC Approved:
DRC Approved:

Name:
Harmonizome (SmartAPI)
Creator: LINCS
Date Modified: 1/31/2023
DCC Approved:
DRC Approved:

Name:
L1000CDS2 (SmartAPI)
Creator: LINCS
Date Modified: 1/31/2023
DCC Approved:
DRC Approved:

Name:
L1000FWD (SmartAPI)
Creator: LINCS
Date Modified: 1/31/2023
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Data (SmartAPI)
Creator: LINCS
Date Modified: 5/22/2022
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Metadata (SmartAPI)
Creator: LINCS
Date Modified: 5/22/2022
DCC Approved:
DRC Approved:

Archived

Name:
FAIRshake (SmartAPI)
Creator: LINCS
Date Modified: 8/7/2018
DCC Approved:
DRC Approved:

Entity Pages

4 Current File(s) | 0 Archived File(s)

4 Current File(s)

0 Archived File(s)

Modified 3/8/2024

Current

Name:
Drugmonizome Drug Pages
Template | Example
Creator: LINCS
Date Modified: 3/8/2024
DCC Approved:
DRC Approved:

Name:
Harmonizome Gene Pages
Template | Example
Creator: LINCS
Date Modified: 3/8/2024
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Drug Pages
Template | Example
Creator: LINCS
Date Modified: 3/8/2024
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Gene Pages
Template | Example
Creator: LINCS
Date Modified: 3/8/2024
DCC Approved:
DRC Approved:

Archived

None Available

PWB Metanodes

3 Current File(s) | 1 Archived File(s)

3 Current File(s)

1 Archived File(s)

Modified 2/26/2024

Current

Name:
LINCS L1000 Reverse Search
Creator: LINCS
Date Modified: 7/19/2023
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Gene Set Search Results
Creator: LINCS
Date Modified: 2/7/2024
DCC Approved:
DRC Approved:

Name:
SigCom LINCS Signature Search Results
Creator: LINCS
Date Modified: 2/7/2024
DCC Approved:
DRC Approved:

Archived

Name:
LINCS L1000 Reverse Search
Creator: LINCS
Date Modified: 2/26/2024
DCC Approved:
DRC Approved:

Chatbot Specifications

0 Available Files

Current

None Available

Archived

None Available

Apps URLs

1 Current File(s) | 0 Archived File(s)

1 Current File(s)

0 Archived File(s)

Modified 6/11/2024

Current

Name:
LINCS Tools Marketplace
Creator: LINCS
Date Modified: 6/11/2024
DCC Approved:
DRC Approved:

Archived

None Available

Library of Integrated Network-based Cellular Signatures (LINCS)

TRAINING & OUTREACH

Application deadline: February 1, 2025

Starts: August 8, 2024

Landmark Publication

Metadata and Processed Data Files

Current

Archived

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Current

Archived

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Archived

Interoperability Assets

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Assets

Consortium

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