All LINCS Production Phase L1000 data generated by the Broad Institute is posted at the NCBIs Gene Expression Omnibus (GEO). Standard NIH data access rules apply – data is freely accessible by anyone (GEO BioProject ID PRJNA290347)
The website lincscloud.org, a Broad Institute developed resource for analysis of LINCS Phase 1 (2011-2014) data, will be deprecated in 2015 as the NIH has recently funded a separate LINCS Data Coordination and Integration Center (DCIC).
Our historic license is given below for reference, but the official information on access to all LINCS resources via the DCIC is available at lincsproject.org.
Access Keys, Code, and Data Files are provided on the following terms:
- Access Keys, Code, and Data Files are single user and assigned to the particular named individual during registration.If anyone else in your group seeks access, please have them fill out the request and we will be glad to provide another personalized key.
- You agree to not redistribute Access Keys, Code, and Data FilesAccess to these resources is restricted to use by you within your research group. Please do not redistribute them.If you have a derivative work that is significantly different from what we provide and you would like to distribute it, please contact us with the details. Our goal is to encourage significant improvements while maintaining provenance and reproducible research standards.
- Any discoveries you make in the data are yoursWe encourage you to publish results from analysis of these data. Please see “Publication Policy” below.
- Access Keys, Code, and Data Files are for research use onlyUsage of Access Keys, Code, and Data Files are restricted to academic use within not-for-profit institutions.
A LINCS-wide publication policy is in development. Until then, these are our (Broad Institute) policies.
The L1000 assay, dataset, and methods are in preparation for publication.
However, we are glad if you have found the data to be useful and would like to incorporate it into your paper. You do not need to wait for the Broad CMap group to first publish a paper. The only exception to this is a paper describing the overall contours of the LINCS dataset (i.e., the manuscript that we at the Broad are working on in collaboration with LINCS). This approach is similar to how The Cancer Genome Atlas (TCGA) policy works – a user can incorporate TCGA findings with respect to a gene of interest prior to the TCGA official paper, but he/she can’t publish on the entire landscape of the TCGA breast cancer dataset (until the lead centers publish).
If your paper needs a citation to our work on L1000 or LINCS, please contact us at firstname.lastname@example.org.
Examples of groups that have published their work on this basis include:
- Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr., Whitesell L, Lindquist S. Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science. 2013/7/19. 341(6143), (2013). Download paper.
- Johannessen CM, Johnson LA, Piccioni F, Townes A, Frederick DT, Donahue MK, Narayan R, Flaherty KT, Wargo JA, Root DE, Garraway LA. A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Nature. 2013/12/5. 504(7478):138-42, (2013). Download paper.
- Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, Shamji AF. Multiplex cytological profiling assay to measure diverse cellular states. PLoS One. 2013/12/2;8(12):e80999, (2013). Download paper.
- Wawer, MJ, Jaramillo DE, Dancik V, Fass DM, Haggarty SJ, Shamji AF, Wagner BK, Schreiber SL, Clemons PA, et al. Automated Structure-Activity Relationship Mining: Connecting chemical structure to biological profiles. J. Biomol. Screen. 2014/4/7, (2014). Download paper.
Please note that as the L1000 and LINCS datasets mature we will revisit these terms. For now, given the evolving nature of the project, we request you contact us (or the LINCS program at NIH) directly if you have any questions on data access.
Because we make these fundamental research results available for free, we cannot bear any risk associated with your use of the data or its results. Further, in order to achieve some protection from unexpected and unforeseeable circumstances, MIT must disclaim its liabilities and damages in accordance with the laws governing software licensing. Please do not allow this legal requirement to discourage your use of the Connectivity Map website.
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