OpenScientificCodeRegistry/Database
Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/rl4m/keap",4 "url": "https://github.com/RL4M/KeAP",5 "host": "github.com",6 "commit": "9130752d602b7128718247ead82a1ddb7514f934",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "16c81ce46aad4d4f4741458f0046ec9d3c5729dd8e39f1a36708c2cfe752d971",14 "language": "License",15 "lines": 21,16 "truncated": false,17 "block": 3,18 "row": 791019 },20 {21 "path": "README.md",22 "sha256": "3e723719936260323d606238d5b5d332d3bc2c74b03009316cbfeeb3752c96f3",23 "language": "Text",24 "lines": 144,25 "truncated": false,26 "block": 4,27 "row": 262028 },29 {30 "path": "gen_onto_protein_data.py",31 "sha256": "edf33c34bbfe2592cb2a668fd21b12b2ca1df1a8928bfbb4a489a4c367b54954",32 "language": "Python",33 "lines": 295,34 "truncated": false,35 "block": 3,36 "row": 2553937 },38 {39 "path": "replace_code/deepspeed.py",40 "sha256": "560288ba8ce29507e09f6c08daf087801c246c934b6e49df44d058af2ff24133",41 "language": "Python",42 "lines": 409,43 "truncated": false,44 "block": 3,45 "row": 2678446 },47 {48 "path": "replace_code/tape/modeling_utils.py",49 "sha256": "730bf8d86fcf022395f824e2c7c40d5db1c16c65d8227e860b18ee14d9a4e5c2",50 "language": "Python",51 "lines": 934,52 "truncated": false,53 "block": 3,54 "row": 2784855 },56 {57 "path": "run_downstream.py",58 "sha256": "edd5bf07f88065fd4abf97b4f0d08477a5b781029aaebbe34cb95e74f2c00479",59 "language": "Python",60 "lines": 283,61 "truncated": false,62 "block": 3,63 "row": 2545764 },65 {66 "path": "run_main.sh",67 "sha256": "19c1b90d3bc04ba603ff62cc1c800a1a60c4c7f513289cbbbbaeb90eb231f7dc",68 "language": "Shell",69 "lines": 61,70 "truncated": false,71 "block": 4,72 "row": 196973 },74 {75 "path": "run_pretrain.py",76 "sha256": "b82aec235796a4060e93d6e21b43ba8239f8779d3744567d9d845c954473fdef",77 "language": "Python",78 "lines": 118,79 "truncated": false,80 "block": 3,81 "row": 2253082 },83 {84 "path": "run_stability.py",85 "sha256": "89728fb500ba0c6997cfd40bcfcd3f7dbfd696bbbab121c4535432482a95b008",86 "language": "Python",87 "lines": 276,88 "truncated": false,89 "block": 3,90 "row": 2534191 },92 {93 "path": "run_stability.sh",94 "sha256": "6a2aedb77ed073db6863cadb9b5176da1ebb02f0d098a2a7e5c946f8bcc98019",95 "language": "Shell",96 "lines": 68,97 "truncated": false,98 "block": 4,99 "row": 2034100 },101 {102 "path": "script/run_contact.sh",103 "sha256": "508b2aa31eda5caa6eb1dfcdd52de5fb5659b9b87be1ed21b6a0b5bed434994b",104 "language": "Shell",105 "lines": 15,106 "truncated": false,107 "block": 4,108 "row": 1535109 },110 {111 "path": "script/run_fluorescence.sh",112 "sha256": "f1e407006dd629e41d5625748b33b1a2921aa85726bf3db8aa3dd23b51c6e953",113 "language": "Shell",114 "lines": 16,115 "truncated": false,116 "block": 4,117 "row": 1557118 },119 {120 "path": "script/run_pretrain.sh",121 "sha256": "b8afd535e5d08e569c43d43c3b29564ac81f54e22c5aff9c5c3fb1094b1be27d",122 "language": "Shell",123 "lines": 106,124 "truncated": false,125 "block": 4,126 "row": 2076127 },128 {129 "path": "script/run_remote_homology.sh",130 "sha256": "8e32a2f19bf371554dfd562cf0dcc168ee920ff6a86c90f1e319e299eafa4c74",131 "language": "Shell",132 "lines": 16,133 "truncated": false,134 "block": 4,135 "row": 1565136 },137 {138 "path": "script/run_ss3.sh",139 "sha256": "c56f23bb470fc11a05c5ccb337568abe8638b4f826336ec43e84f5645a4c95c4",140 "language": "Shell",141 "lines": 15,142 "truncated": false,143 "block": 4,144 "row": 1520145 },146 {147 "path": "script/run_ss8.sh",148 "sha256": "beaf6ca04b16c154e346623d87aaf85c360fe8bf0478e6706cf4d76390780330",149 "language": "Shell",150 "lines": 15,151 "truncated": false,152 "block": 4,153 "row": 1519154 },155 {156 "path": "script/run_stability.sh",157 "sha256": "f1e138c5fbe326b8272318a3f6e4ecf898880d77bbd561044490d3a91e28e2fb",158 "language": "Shell",159 "lines": 16,160 "truncated": false,161 "block": 4,162 "row": 1558163 },164 {165 "path": "src/benchmark/GNN_PPI/extract_protein_embeddings.py",166 "sha256": "ba88c59cf165af6e1bf1533f874e61440758bf474559cc080f91d31410279f90",167 "language": "Python",168 "lines": 288,169 "truncated": false,170 "block": 3,171 "row": 25607172 },173 {174 "path": "src/benchmark/GNN_PPI/gnn_data.py",175 "sha256": "488e4166c2005e7f2dfed06395b2587c65610da5586f5e1922419f77527880a5",176 "language": "Python",177 "lines": 296,178 "truncated": false,179 "block": 3,180 "row": 25747181 },182 {183 "path": "src/benchmark/GNN_PPI/gnn_model.py",184 "sha256": "44187126c80787d1bbeb88e0ab7c99a5b91ba6bef70266e54327d5b360ae9112",185 "language": "Python",186 "lines": 194,187 "truncated": false,188 "block": 3,189 "row": 23694190 },191 {192 "path": "src/benchmark/GNN_PPI/gnn_test.py",193 "sha256": "3d160eb7c1123a4e969830b01b1f33bd094454559b3e0aeee17cc649af687a46",194 "language": "Python",195 "lines": 169,196 "truncated": false,197 "block": 3,198 "row": 23417199 },200 {201 "path": "src/benchmark/GNN_PPI/gnn_train.py",202 "sha256": "279559af57f1106e02aedf545aabf3763d15b480bb382b6d3de0b950a7b2f03d",203 "language": "Python",204 "lines": 264,205 "truncated": false,206 "block": 3,207 "row": 25530208 },209 {210 "path": "src/benchmark/GNN_PPI/run.py",211 "sha256": "720c03a4706eee7645cd182093740c295da3c657bc6080bf1f76872181bf8da0",212 "language": "Python",213 "lines": 45,214 "truncated": false,215 "block": 3,216 "row": 19821217 },218 {219 "path": "src/benchmark/GNN_PPI/run_test.py",220 "sha256": "db0d9bcc26880c5b3c7f3b9e04423c7080a4a0a3ef7080fb3241b55ab6f1fa88",221 "language": "Python",222 "lines": 31,223 "truncated": false,224 "block": 3,225 "row": 19176226 },227 {228 "path": "src/benchmark/GNN_PPI/utils.py",229 "sha256": "818d1c650b0ea247b07c2d0d7cfe4a4da3cea9459b897d590712cd2446c4905b",230 "language": "Python",231 "lines": 165,232 "truncated": false,233 "block": 3,234 "row": 23378235 },236 {237 "path": "src/benchmark/PROBE/bin/PROBE.py",238 "sha256": "62934ff8ebea13fac429aa48f975dff5837b9639286af1aec9cade0ccb54d4f4",239 "language": "Python",240 "lines": 62,241 "truncated": false,242 "block": 3,243 "row": 21276244 },245 {246 "path": "src/benchmark/PROBE/bin/binding_affinity_estimator.py",247 "sha256": "03327199697929c71462f3d503cc238ca67117bc191d4c21c8ccbe95279195cb",248 "language": "Python",249 "lines": 189,250 "truncated": false,251 "block": 3,252 "row": 24755253 },254 {255 "path": "src/benchmark/PROBE/bin/function_predictor.py",256 "sha256": "413267ffb764e70d6a91af15d1d05980e04616d6bf12425abab72f0618d9e6e9",257 "language": "Python",258 "lines": 216,259 "truncated": false,260 "block": 3,261 "row": 25758262 },263 {264 "path": "src/benchmark/PROBE/bin/semantic_similarity_infer.py",265 "sha256": "d837e9ccce6af629edaba328049ead669ddaff2d05bfb9cfd0e1120cc0fd637e",266 "language": "Python",267 "lines": 160,268 "truncated": false,269 "block": 3,270 "row": 24424271 },272 {273 "path": "src/benchmark/PROBE/bin/target_family_classifier.py",274 "sha256": "cb1916ffc92a44ef148c96e58cfecb15963c79240c4b7b909433ba36f46b33f7",275 "language": "Python",276 "lines": 226,277 "truncated": false,278 "block": 3,279 "row": 25004280 },281 {282 "path": "src/benchmark/PROBE/extract_embeddings.py",283 "sha256": "a4f0f67ebe59d3a6599035ff9622cb9a71a9a051c20c2bb1974d0f43127064ce",284 "language": "Python",285 "lines": 354,286 "truncated": false,287 "block": 3,288 "row": 26033289 },290 {291 "path": "src/benchmark/dataset.py",292 "sha256": "bd5ce6366ff8000164d14ce5287f102af5f6f86cf4d25964f10eaab4164c2fbb",293 "language": "Python",294 "lines": 533,295 "truncated": false,296 "block": 3,297 "row": 26969298 },299 {300 "path": "src/benchmark/metrics.py",301 "sha256": "0afecc5caa929c1bc5daec4a990e65e55023b1d80d581da32d7c833c8a8e0e48",302 "language": "Python",303 "lines": 91,304 "truncated": false,305 "block": 3,306 "row": 21237307 },308 {309 "path": "src/benchmark/models.py",310 "sha256": "7f3b0b687ae5022168c171baa3978a41e3ddb03d148814cbcc264536c1c6392c",311 "language": "Python",312 "lines": 233,313 "truncated": false,314 "block": 3,315 "row": 24813316 },317 {318 "path": "src/benchmark/trainer.py",319 "sha256": "b8598423388edebe46d7eb2e7cbd07e750885bc76886f92c44a2871267c98722",320 "language": "Python",321 "lines": 279,322 "truncated": false,323 "block": 3,324 "row": 26116325 },326 {327 "path": "src/dataloader.py",328 "sha256": "d5a6b726fa8b1e3e07fd2c3f4c4e1e7b70f0a7718b2d577a048c8a97d4fa592c",329 "language": "Python",330 "lines": 407,331 "truncated": false,332 "block": 3,333 "row": 27000334 },335 {336 "path": "src/dataset.py",337 "sha256": "ff7ebd57c280c24a6e560d90a591209c52606f7814688ec9e5e0f1ca2892bdff",338 "language": "Python",339 "lines": 466,340 "truncated": false,341 "block": 3,342 "row": 27019343 },344 {345 "path": "src/decoder.py",346 "sha256": "28dd7032c0afc45b54a7c6c8d60a29265e725854ae5f39e9b7a147dfb6b23ad7",347 "language": "Python",348 "lines": 748,349 "truncated": false,350 "block": 3,351 "row": 27748352 },353 {354 "path": "src/models.py",355 "sha256": "f288321afab713c1066cb949188e7f0141fb38253a61526d7c995166d0f2755e",356 "language": "Python",357 "lines": 513,358 "truncated": false,359 "block": 3,360 "row": 27142361 },362 {363 "path": "src/op_deepspeed.py",364 "sha256": "8acfe8a927f7c960523b783838d6d48dbff9ba4bc2e7f325fb673b391ce39b74",365 "language": "Python",366 "lines": 64,367 "truncated": false,368 "block": 3,369 "row": 21943370 },371 {372 "path": "src/optimization.py",373 "sha256": "2c5c025d40c6cf03765118a906e57c96d7db4d9394dcc1f52a6f02b2e5b5dd5a",374 "language": "Python",375 "lines": 84,376 "truncated": false,377 "block": 3,378 "row": 21550379 },380 {381 "path": "src/sampling.py",382 "sha256": "087fe3ce39013afc1591583bec8be8f3cb6a885ff84a51dbd39ca2188c747627",383 "language": "Python",384 "lines": 55,385 "truncated": false,386 "block": 3,387 "row": 20101388 },389 {390 "path": "src/trainer.py",391 "sha256": "b9c59ac8cc6154b2f6001e5ba4a2f272ea9a0c8fa27ba09bfc86a359f2539c53",392 "language": "Python",393 "lines": 677,394 "truncated": false,395 "block": 3,396 "row": 27611397 },398 {399 "path": "src/training_args.py",400 "sha256": "64f443bad196c8f0be4b6e4f13ebb5dc2e577780f6ff5b1765661160c0b8bfef",401 "language": "Python",402 "lines": 319,403 "truncated": false,404 "block": 3,405 "row": 25624406 }407 ]408}