Merge pull request #272 from rseng/update/software-2022-03-27

Update from update/software-2022-03-27
rseng · Mar 27, 2022 · 381384b · 381384b
2 parents 41b31fc + 4fd1d7a
commit 381384b
Show file tree

Hide file tree

Showing 60 changed files with 6,727 additions and 2 deletions.
diff --git a/database/github/AlphonsG/Rainbow-Optical-Flow-For-ALI/metadata.json b/database/github/AlphonsG/Rainbow-Optical-Flow-For-ALI/metadata.json
@@ -0,0 +1,47 @@
+{
+    "parser": "github",
+    "uid": "github/AlphonsG/Rainbow-Optical-Flow-For-ALI",
+    "url": "https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI",
+    "data": {
+        "timestamp": "2022-03-27 00:52:25.584407",
+        "name": "Rainbow-Optical-Flow-For-ALI",
+        "url": "https://api.github.com/repos/AlphonsG/Rainbow-Optical-Flow-For-ALI",
+        "full_name": "AlphonsG/Rainbow-Optical-Flow-For-ALI",
+        "html_url": "https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI",
+        "private": false,
+        "description": "Repository for software detailed in 'Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow' software paper. See Readme for more details.",
+        "created_at": "2021-03-26T09:39:17Z",
+        "updated_at": "2021-12-10T01:48:54Z",
+        "clone_url": "https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI.git",
+        "homepage": "",
+        "size": 551852,
+        "stargazers_count": 3,
+        "watchers_count": 3,
+        "language": "Python",
+        "open_issues_count": 2,
+        "license": {
+            "key": "mit",
+            "name": "MIT License",
+            "spdx_id": "MIT",
+            "url": "https://api.github.com/licenses/mit",
+            "node_id": "MDc6TGljZW5zZTEz"
+        },
+        "subscribers_count": 3,
+        "owner": {
+            "html_url": "https://github.com/AlphonsG",
+            "avatar_url": "https://avatars.githubusercontent.com/u/45003643?v=4",
+            "login": "AlphonsG",
+            "type": "User"
+        },
+        "topics": [
+            "deep-learning",
+            "biology",
+            "image-analysis",
+            "bioinformatics",
+            "optical-flow",
+            "python",
+            "pytorch"
+        ]
+    },
+    "doi": "https://doi.org/10.5281/zenodo.6355080"
+}
diff --git a/database/github/BU-ISCIII/iSkyLIMS/metadata.json b/database/github/BU-ISCIII/iSkyLIMS/metadata.json
@@ -0,0 +1,45 @@
+{
+    "parser": "github",
+    "uid": "github/BU-ISCIII/iSkyLIMS",
+    "url": "https://github.com/BU-ISCIII/iSkyLIMS",
+    "data": {
+        "timestamp": "2022-03-27 00:53:35.464286",
+        "name": "iSkyLIMS",
+        "url": "https://api.github.com/repos/BU-ISCIII/iSkyLIMS",
+        "full_name": "BU-ISCIII/iSkyLIMS",
+        "html_url": "https://github.com/BU-ISCIII/iSkyLIMS",
+        "private": false,
+        "description": "is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.",
+        "created_at": "2018-05-10T14:17:06Z",
+        "updated_at": "2022-03-04T14:20:18Z",
+        "clone_url": "https://github.com/BU-ISCIII/iSkyLIMS.git",
+        "homepage": "https://github.com/BU-ISCIII/iSkyLIMS/wiki",
+        "size": 20027,
+        "stargazers_count": 32,
+        "watchers_count": 32,
+        "language": "JavaScript",
+        "open_issues_count": 19,
+        "license": {
+            "key": "gpl-3.0",
+            "name": "GNU General Public License v3.0",
+            "spdx_id": "GPL-3.0",
+            "url": "https://api.github.com/licenses/gpl-3.0",
+            "node_id": "MDc6TGljZW5zZTk="
+        },
+        "subscribers_count": 8,
+        "owner": {
+            "html_url": "https://github.com/BU-ISCIII",
+            "avatar_url": "https://avatars.githubusercontent.com/u/29040266?v=4",
+            "login": "BU-ISCIII",
+            "type": "Organization"
+        },
+        "topics": [
+            "bioinformatics-analysis",
+            "lims",
+            "workflow",
+            "ngs-analysis",
+            "ngs",
+            "ngs-data"
+        ]
+    }
+}
diff --git a/database/github/BU-ISCIII/plasmidID/metadata.json b/database/github/BU-ISCIII/plasmidID/metadata.json
@@ -0,0 +1,44 @@
+{
+    "parser": "github",
+    "uid": "github/BU-ISCIII/plasmidID",
+    "url": "https://github.com/BU-ISCIII/plasmidID",
+    "data": {
+        "timestamp": "2022-03-27 00:53:34.971476",
+        "name": "plasmidID",
+        "url": "https://api.github.com/repos/BU-ISCIII/plasmidID",
+        "full_name": "BU-ISCIII/plasmidID",
+        "html_url": "https://github.com/BU-ISCIII/plasmidID",
+        "private": false,
+        "description": "PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.",
+        "created_at": "2018-05-30T14:49:49Z",
+        "updated_at": "2022-03-24T22:39:28Z",
+        "clone_url": "https://github.com/BU-ISCIII/plasmidID.git",
+        "homepage": "https://github.com/BU-ISCIII/plasmidID/wiki",
+        "size": 96256,
+        "stargazers_count": 26,
+        "watchers_count": 26,
+        "language": "Shell",
+        "open_issues_count": 1,
+        "license": {
+            "key": "gpl-3.0",
+            "name": "GNU General Public License v3.0",
+            "spdx_id": "GPL-3.0",
+            "url": "https://api.github.com/licenses/gpl-3.0",
+            "node_id": "MDc6TGljZW5zZTk="
+        },
+        "subscribers_count": 4,
+        "owner": {
+            "html_url": "https://github.com/BU-ISCIII",
+            "avatar_url": "https://avatars.githubusercontent.com/u/29040266?v=4",
+            "login": "BU-ISCIII",
+            "type": "Organization"
+        },
+        "topics": [
+            "plasmid",
+            "ngs",
+            "ngs-analysis",
+            "microbiology",
+            "whole-genome-sequencing"
+        ]
+    }
+}
diff --git a/database/github/BU-ISCIII/taranis/metadata.json b/database/github/BU-ISCIII/taranis/metadata.json
@@ -0,0 +1,46 @@
+{
+    "parser": "github",
+    "uid": "github/BU-ISCIII/taranis",
+    "url": "https://github.com/BU-ISCIII/taranis",
+    "data": {
+        "timestamp": "2022-03-27 00:53:35.943943",
+        "name": "taranis",
+        "url": "https://api.github.com/repos/BU-ISCIII/taranis",
+        "full_name": "BU-ISCIII/taranis",
+        "html_url": "https://github.com/BU-ISCIII/taranis",
+        "private": false,
+        "description": "cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.",
+        "created_at": "2018-10-17T15:00:53Z",
+        "updated_at": "2022-03-13T12:07:01Z",
+        "clone_url": "https://github.com/BU-ISCIII/taranis.git",
+        "homepage": "",
+        "size": 3484,
+        "stargazers_count": 3,
+        "watchers_count": 3,
+        "language": "Python",
+        "open_issues_count": 0,
+        "license": {
+            "key": "gpl-3.0",
+            "name": "GNU General Public License v3.0",
+            "spdx_id": "GPL-3.0",
+            "url": "https://api.github.com/licenses/gpl-3.0",
+            "node_id": "MDc6TGljZW5zZTk="
+        },
+        "subscribers_count": 4,
+        "owner": {
+            "html_url": "https://github.com/BU-ISCIII",
+            "avatar_url": "https://avatars.githubusercontent.com/u/29040266?v=4",
+            "login": "BU-ISCIII",
+            "type": "Organization"
+        },
+        "topics": [
+            "sequencing",
+            "cgmlst",
+            "wgmlst",
+            "mlst",
+            "bacterial-genomes",
+            "outbreak-data-analysis",
+            "outbreak-detection"
+        ]
+    }
+}
diff --git a/database/github/FSEC-Photovoltaics/pvrpm-lcoe/metadata.json b/database/github/FSEC-Photovoltaics/pvrpm-lcoe/metadata.json
@@ -0,0 +1,39 @@
+{
+    "parser": "github",
+    "uid": "github/FSEC-Photovoltaics/pvrpm-lcoe",
+    "url": "https://github.com/FSEC-Photovoltaics/pvrpm-lcoe",
+    "data": {
+        "timestamp": "2022-03-27 00:52:26.066663",
+        "name": "pvrpm-lcoe",
+        "url": "https://api.github.com/repos/FSEC-Photovoltaics/pvrpm-lcoe",
+        "full_name": "FSEC-Photovoltaics/pvrpm-lcoe",
+        "html_url": "https://github.com/FSEC-Photovoltaics/pvrpm-lcoe",
+        "private": false,
+        "description": "PV Simulation using SAM and Python",
+        "created_at": "2021-06-03T15:49:06Z",
+        "updated_at": "2022-03-02T00:35:43Z",
+        "clone_url": "https://github.com/FSEC-Photovoltaics/pvrpm-lcoe.git",
+        "homepage": "",
+        "size": 7131,
+        "stargazers_count": 2,
+        "watchers_count": 2,
+        "language": "Python",
+        "open_issues_count": 4,
+        "license": {
+            "key": "bsd-3-clause",
+            "name": "BSD 3-Clause \"New\" or \"Revised\" License",
+            "spdx_id": "BSD-3-Clause",
+            "url": "https://api.github.com/licenses/bsd-3-clause",
+            "node_id": "MDc6TGljZW5zZTU="
+        },
+        "subscribers_count": 3,
+        "owner": {
+            "html_url": "https://github.com/FSEC-Photovoltaics",
+            "avatar_url": "https://avatars.githubusercontent.com/u/72280691?v=4",
+            "login": "FSEC-Photovoltaics",
+            "type": "Organization"
+        },
+        "topics": []
+    },
+    "doi": "https://doi.org/10.5281/zenodo.6355115"
+}
diff --git a/database/github/HillLab/SomaticSiMu/metadata.json b/database/github/HillLab/SomaticSiMu/metadata.json
@@ -0,0 +1,43 @@
+{
+    "parser": "github",
+    "uid": "github/HillLab/SomaticSiMu",
+    "url": "https://github.com/HillLab/SomaticSiMu",
+    "data": {
+        "timestamp": "2022-03-27 00:53:32.149603",
+        "name": "SomaticSiMu",
+        "url": "https://api.github.com/repos/HillLab/SomaticSiMu",
+        "full_name": "HillLab/SomaticSiMu",
+        "html_url": "https://github.com/HillLab/SomaticSiMu",
+        "private": false,
+        "description": "SomaticSiMu generates single and double base pair substitutions, and single base pair insertions and deletions of biologically representative mutation signature probabilities and combinations.",
+        "created_at": "2020-08-17T22:33:29Z",
+        "updated_at": "2022-03-09T15:11:52Z",
+        "clone_url": "https://github.com/HillLab/SomaticSiMu.git",
+        "homepage": "",
+        "size": 166147,
+        "stargazers_count": 3,
+        "watchers_count": 3,
+        "language": "Python",
+        "open_issues_count": 0,
+        "license": {
+            "key": "other",
+            "name": "Other",
+            "spdx_id": "NOASSERTION",
+            "url": null,
+            "node_id": "MDc6TGljZW5zZTA="
+        },
+        "subscribers_count": 1,
+        "owner": {
+            "html_url": "https://github.com/HillLab",
+            "avatar_url": "https://avatars.githubusercontent.com/u/69210731?v=4",
+            "login": "HillLab",
+            "type": "Organization"
+        },
+        "topics": [
+            "simulation",
+            "signature",
+            "mutation"
+        ]
+    },
+    "doi": "10.1093/bioinformatics/btac128"
+}
diff --git a/database/github/PMBio/spatialde2-paper/metadata.json b/database/github/PMBio/spatialde2-paper/metadata.json
@@ -0,0 +1,33 @@
+{
+    "parser": "github",
+    "uid": "github/PMBio/spatialde2-paper",
+    "url": "https://github.com/PMBio/spatialde2-paper",
+    "data": {
+        "timestamp": "2022-03-27 00:53:34.495914",
+        "name": "spatialde2-paper",
+        "url": "https://api.github.com/repos/PMBio/spatialde2-paper",
+        "full_name": "PMBio/spatialde2-paper",
+        "html_url": "https://github.com/PMBio/spatialde2-paper",
+        "private": false,
+        "description": "Code to reproduce the figures (data not included)",
+        "created_at": "2021-08-26T13:15:00Z",
+        "updated_at": "2021-10-26T14:20:12Z",
+        "clone_url": "https://github.com/PMBio/spatialde2-paper.git",
+        "homepage": null,
+        "size": 2895,
+        "stargazers_count": 0,
+        "watchers_count": 0,
+        "language": "Jupyter Notebook",
+        "open_issues_count": 0,
+        "license": null,
+        "subscribers_count": 1,
+        "owner": {
+            "html_url": "https://github.com/PMBio",
+            "avatar_url": "https://avatars.githubusercontent.com/u/578044?v=4",
+            "login": "PMBio",
+            "type": "Organization"
+        },
+        "topics": []
+    },
+    "doi": "10.1101/2021.10.27.466045"
+}
diff --git a/database/github/arcaldwell49/SimplyAgree/metadata.json b/database/github/arcaldwell49/SimplyAgree/metadata.json
@@ -0,0 +1,39 @@
+{
+    "parser": "github",
+    "uid": "github/arcaldwell49/SimplyAgree",
+    "url": "https://github.com/arcaldwell49/SimplyAgree",
+    "data": {
+        "timestamp": "2022-03-27 00:52:24.935242",
+        "name": "SimplyAgree",
+        "url": "https://api.github.com/repos/arcaldwell49/SimplyAgree",
+        "full_name": "arcaldwell49/SimplyAgree",
+        "html_url": "https://github.com/arcaldwell49/SimplyAgree",
+        "private": false,
+        "description": "A simple R package for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement",
+        "created_at": "2020-03-05T14:01:14Z",
+        "updated_at": "2022-03-11T00:50:07Z",
+        "clone_url": "https://github.com/arcaldwell49/SimplyAgree.git",
+        "homepage": "",
+        "size": 87400,
+        "stargazers_count": 1,
+        "watchers_count": 1,
+        "language": "HTML",
+        "open_issues_count": 4,
+        "license": {
+            "key": "gpl-3.0",
+            "name": "GNU General Public License v3.0",
+            "spdx_id": "GPL-3.0",
+            "url": "https://api.github.com/licenses/gpl-3.0",
+            "node_id": "MDc6TGljZW5zZTk="
+        },
+        "subscribers_count": 1,
+        "owner": {
+            "html_url": "https://github.com/arcaldwell49",
+            "avatar_url": "https://avatars.githubusercontent.com/u/24322628?v=4",
+            "login": "arcaldwell49",
+            "type": "User"
+        },
+        "topics": []
+    },
+    "doi": "https://doi.org/10.5281/zenodo.6338611"
+}