From 21ead96916059be156a5c2d9024f054fb5c7b15d Mon Sep 17 00:00:00 2001 From: gwaygenomics Date: Tue, 12 May 2020 11:30:00 -0400 Subject: [PATCH 1/5] add dual license --- LICENSE_BSD3.md | 29 ++++++++++++ LICENSE_CC0.md | 121 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 LICENSE_BSD3.md create mode 100644 LICENSE_CC0.md diff --git a/LICENSE_BSD3.md b/LICENSE_BSD3.md new file mode 100644 index 0000000..5844197 --- /dev/null +++ b/LICENSE_BSD3.md @@ -0,0 +1,29 @@ +# BSD 3-Clause License + +_Copyright (c) 2020, The Broad Institute of MIT and Harvard_ +_All rights reserved._ + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. 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From 3f9d5c87b801f6d060f0f3216c9b9c0ef9af33f8 Mon Sep 17 00:00:00 2001 From: gwaygenomics Date: Tue, 12 May 2020 11:30:18 -0400 Subject: [PATCH 2/5] add dual license note in README --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index e4280de..d6aa82b 100644 --- a/README.md +++ b/README.md @@ -30,3 +30,8 @@ conda activate lincs ``` Also note that when contributing to the repository, make sure to add any new package in the `environment.yml` file. + +## License + +We use a dual license in this repository. +We license the source code as [BSD 3-Clause](LICENSE_BSD3.md), and license the data, results, and figures as [CC0 1.0](LICENSE_CC0.md). From 308207c6b1d2d76efbde1822accd3fb4aaf68042 Mon Sep 17 00:00:00 2001 From: Shantanu Singh Date: Tue, 12 May 2020 15:38:56 -0400 Subject: [PATCH 3/5] Add credits and other edits. --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d6aa82b..a7c1682 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,14 @@ -# Processed Cell Painting Data for the LINCS Drug Repurposing Project +# Processed Data for the LINCS Cell Painting Project -The repository stores data and data processing scripts for **a subset** of the LINCS Drug Repurposing Project. -In this project, we perturbed A549 cells with ~1,500 compounds across 6 doses with ~4 biological replicates. +The repository stores data and data processing scripts for **a subset** of the [Broad Drug Repurposing Hub](https://clue.io/repurposing#home) collection of compounds. + +In this project, the [Connectivity Map](https://clue.io/team) perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. We refer to this dataset as `LINCS Pilot 1`. For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). ## Image-Based Profiling -We apply a unified, image-based profiling pipeline to all Drug Repurposing Hub Cell Painting plates. +We apply a unified, image-based profiling pipeline to all 136 384-well plates from `LINCS Pilot 1` . We use [pycytominer](https://github.com/cytomining/pycytominer) as the primary tool for image-based profiling. The profiles are processed and stored in the [profiles/](profiles/) directory. From f5a82b1e0b4b52d5aa19854e8da68e250e32d8b2 Mon Sep 17 00:00:00 2001 From: Shantanu Singh Date: Tue, 12 May 2020 15:52:33 -0400 Subject: [PATCH 4/5] Cite clue.io as the primary source --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a7c1682..17f2cf5 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ The repository stores data and data processing scripts for **a subset** of the [Broad Drug Repurposing Hub](https://clue.io/repurposing#home) collection of compounds. -In this project, the [Connectivity Map](https://clue.io/team) perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. We refer to this dataset as `LINCS Pilot 1`. +In this project, the [Connectivity Map](https://clue.io/team) team perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. We refer to this dataset as `LINCS Pilot 1`. -For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). +For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). Information about the compounds can be interactively explored in the [CLUE Repurposing app](https://clue.io/repurposing-app). The [Morphology Connectivity Hub](https://clue.io/morphology) is the primary source of this dataset. ## Image-Based Profiling From f06cd16639da007cd0177be977ebef5a732a3b68 Mon Sep 17 00:00:00 2001 From: Shantanu Singh Date: Tue, 12 May 2020 18:34:59 -0400 Subject: [PATCH 5/5] one-sentence-per-line https://rhodesmill.org/brandon/2012/one-sentence-per-line/ --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 17f2cf5..31f9b48 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,12 @@ The repository stores data and data processing scripts for **a subset** of the [Broad Drug Repurposing Hub](https://clue.io/repurposing#home) collection of compounds. -In this project, the [Connectivity Map](https://clue.io/team) team perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. We refer to this dataset as `LINCS Pilot 1`. +In this project, the [Connectivity Map](https://clue.io/team) team perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. +We refer to this dataset as `LINCS Pilot 1`. -For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). Information about the compounds can be interactively explored in the [CLUE Repurposing app](https://clue.io/repurposing-app). The [Morphology Connectivity Hub](https://clue.io/morphology) is the primary source of this dataset. +For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). +Information about the compounds can be interactively explored in the [CLUE Repurposing app](https://clue.io/repurposing-app). +The [Morphology Connectivity Hub](https://clue.io/morphology) is the primary source of this dataset. ## Image-Based Profiling