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/zhumetlab/metgenx",4 "url": "https://github.com/ZhuMetLab/MetGenX",5 "host": "github.com",6 "commit": "89dbcb02b44c71b61a54925bb619aa865ea50907",7 "license": "CC-BY-NC-ND-4.0",8 "license_confirmed_by": "license file LICENSE.md",9 "redistribution": "with_conditions",10 "files": [11 {12 "path": "Generation/generate_api.py",13 "sha256": "2987a260fec5ebce0afecb00cc957f43c85e1a7c30bc016a3d26056381c39fdd",14 "language": "Python",15 "lines": 87,16 "truncated": false,17 "block": 9,18 "row": 893319 },20 {21 "path": "Generation/pred_spec.py",22 "sha256": "a67e0ffab34decc2ca8e1511a7bb23a0d41770abcd458b16286c9981c2535497",23 "language": "Python",24 "lines": 185,25 "truncated": false,26 "block": 9,27 "row": 1052028 },29 {30 "path": "LICENSE.md",31 "sha256": "40afb0570049e143a1ca754d19172bfeecdfe256f0339a2862d902ef771d80e8",32 "language": "License",33 "lines": 350,34 "truncated": false,35 "block": 1,36 "row": 222637 },38 {39 "path": "MS2Tools/SpectrumFileReader.py",40 "sha256": "fc87ed46bc2349eaa08295d3777de97e87fbcf04407f7dfe09f82d68a5d1a6cd",41 "language": "Python",42 "lines": 430,43 "truncated": false,44 "block": 9,45 "row": 1163646 },47 {48 "path": "MS2Tools/structure.py",49 "sha256": "a06557d628cc6a7b1dc21959357004a1cb88f6f2a87748af4d7b32ceb994fd90",50 "language": "Python",51 "lines": 84,52 "truncated": false,53 "block": 9,54 "row": 811955 },56 {57 "path": "MS2Tools/util.py",58 "sha256": "a6149867fb4f1c188ca4f150baf3fa126aff6fe6890958edbaecee3d677abd1d",59 "language": "Python",60 "lines": 24,61 "truncated": false,62 "block": 9,63 "row": 683364 },65 {66 "path": "Model/BART/BART.py",67 "sha256": "4c64f927cfdbac4e09f69699d5197d6bd13a1cb04fded974f4dc31558d73d303",68 "language": "Python",69 "lines": 79,70 "truncated": false,71 "block": 9,72 "row": 878973 },74 {75 "path": "Model/BART/BART_transformer.py",76 "sha256": "1ac476441234ad65dff9b93bb19b43e5572ca6658c91dfa83ea0d6c195dfb0bc",77 "language": "Python",78 "lines": 130,79 "truncated": false,80 "block": 9,81 "row": 966682 },83 {84 "path": "Model/BART/Generation.py",85 "sha256": "dfec739aba5016db195f4457d6439b24eddb2092c9b26c3ef9f21b4f0e7db9bd",86 "language": "Python",87 "lines": 195,88 "truncated": false,89 "block": 9,90 "row": 1085191 },92 {93 "path": "Model/BART/base.py",94 "sha256": "3a0ffd93311d61082af521941e268291ff606b8a038d881efd08b4f624d5a2ae",95 "language": "Python",96 "lines": 95,97 "truncated": false,98 "block": 9,99 "row": 9123100 },101 {102 "path": "Model/Configs/config.py",103 "sha256": "64665491c87e1299b6e126057adf5065b42ab8863e1171f891940f73c6e8bb12",104 "language": "Python",105 "lines": 190,106 "truncated": false,107 "block": 9,108 "row": 10090109 },110 {111 "path": "Model/Fingerprints/fingerprint-wrapper/src/ch/moduled/fingerprintwrapper/FingerprintUtil.java",112 "sha256": "18d5920c3799241b4c8e02848cf54cba941dfc21320c768831828aac474113d9",113 "language": "Java",114 "lines": 421,115 "truncated": false,116 "block": 9,117 "row": 2012118 },119 {120 "path": "Model/Fingerprints/fingerprint-wrapper/src/ch/moduled/fingerprintwrapper/FixedFingerprinterInstanceClone.java",121 "sha256": "7e429d5b7fe232d2becabc3bc6acab496a8436840c4500a5c4657832413b007c",122 "language": "Java",123 "lines": 83,124 "truncated": false,125 "block": 9,126 "row": 2008127 },128 {129 "path": "Model/Fingerprints/fingerprint-wrapper/src/ch/moduled/fingerprintwrapper/IPythonPipe.java",130 "sha256": "c30ae722744e4a656d3dd79ef3cd81b7cebc71e28ba20bbebe9fa182f4605d34",131 "language": "Java",132 "lines": 9,133 "truncated": false,134 "block": 9,135 "row": 1984136 },137 {138 "path": "Model/Fingerprints/fingerprint-wrapper/src/ch/moduled/fingerprintwrapper/PythonOutputStream.java",139 "sha256": "0105bd6c122bf63d49789154bc74cc0daad347139262b7dc30d61aaafa775cba",140 "language": "Java",141 "lines": 30,142 "truncated": false,143 "block": 9,144 "row": 2000145 },146 {147 "path": "Model/Fingerprints/fingerprint-wrapper/src/edu/rutgers/sakai/java/util/BitToBoolean.java",148 "sha256": "aabbbb04dd18570af401214932ba178abf8b41a7157d974f5896884981d58cf7",149 "language": "Java",150 "lines": 116,151 "truncated": false,152 "block": 9,153 "row": 2009154 },155 {156 "path": "Model/Fingerprints/fingerprinting.py",157 "sha256": "426c6b731cf1073bd90a48ccdc511b1745154a2cb33407e3c90c7073e0f721ce",158 "language": "Python",159 "lines": 263,160 "truncated": false,161 "block": 9,162 "row": 10516163 },164 {165 "path": "Model/MassSpecGym/BART.py",166 "sha256": "6d8e4b087799cff3febe8be9c33872ef7c8dd67d5faa79b1a56f6cef34aec361",167 "language": "Python",168 "lines": 172,169 "truncated": false,170 "block": 9,171 "row": 10162172 },173 {174 "path": "Model/MassSpecGym/datasets.py",175 "sha256": "7b7ff7042f78b2ce43301d165ec8ef6648e02f032ce039a4d758c4bc2ebe6156",176 "language": "Python",177 "lines": 222,178 "truncated": false,179 "block": 9,180 "row": 10519181 },182 {183 "path": "Model/Prediction.py",184 "sha256": "b21186a6a3d366ceab2b5ab2efeae923531a37b26641e3f23e58ef17cdc01f53",185 "language": "Python",186 "lines": 213,187 "truncated": false,188 "block": 9,189 "row": 10791190 },191 {192 "path": "Model/datasets/ProcessingFormula.py",193 "sha256": "681414818d939bd63c64b52306c9745255ef401d23d4bc19a75d0befad0c69af",194 "language": "Python",195 "lines": 66,196 "truncated": false,197 "block": 9,198 "row": 7920199 },200 {201 "path": "Model/datasets/Tokenizer.py",202 "sha256": "72efe473029aa4b3ab7cecf38116b124d3a5faa532726a306b57f0c4b1f76699",203 "language": "Python",204 "lines": 102,205 "truncated": false,206 "block": 9,207 "row": 9072208 },209 {210 "path": "Model/datasets/Vocabulary.py",211 "sha256": "68208d241148a30bdeb4d569492306be677738f599708f4e56a9c2962e5f97be",212 "language": "Python",213 "lines": 106,214 "truncated": false,215 "block": 9,216 "row": 8989217 },218 {219 "path": "Model/datasets/data_utils.py",220 "sha256": "52148e0671bb791ba15fa4cbc2de8e3e994f25c75b5f0fca4e1d1b0bdd155fcb",221 "language": "Python",222 "lines": 80,223 "truncated": false,224 "block": 9,225 "row": 8434226 },227 {228 "path": "Model/datasets/smiles.py",229 "sha256": "4a43d264f39e7515cd11553b1213117f5627d0db2b3ba18829d6a8892f75ace2",230 "language": "Python",231 "lines": 29,232 "truncated": false,233 "block": 9,234 "row": 7290235 },236 {237 "path": "Model_training/Build_dataset.py",238 "sha256": "d5b0ef06a7d39b852a1b111f9b6754fe74511d6f1758cfd8d06ed44548fca7b9",239 "language": "Python",240 "lines": 77,241 "truncated": false,242 "block": 9,243 "row": 8573244 },245 {246 "path": "Model_training/Embedding_database.py",247 "sha256": "83b8072cab12aff87e8df6b82ffd876d112f7a47e2901f094712883e85263b93",248 "language": "Python",249 "lines": 48,250 "truncated": false,251 "block": 9,252 "row": 7732253 },254 {255 "path": "Model_training/MassSpecGym/Evaluation.py",256 "sha256": "5adcbb4cdd340888889db99efb22ed5f6e92a8c6074f462bb8230a3427794d31",257 "language": "Python",258 "lines": 174,259 "truncated": false,260 "block": 9,261 "row": 10311262 },263 {264 "path": "Model_training/Prediction.py",265 "sha256": "0a666a2815c41bbfbf996cf78c5856d211fedda9ebcc0bdf591562794174f710",266 "language": "Python",267 "lines": 68,268 "truncated": false,269 "block": 9,270 "row": 8570271 },272 {273 "path": "Model_training/RerankModel.py",274 "sha256": "6946ee540c184916c9c88c3ada842c69f6200607eeecba1e37f2197e2dad545f",275 "language": "Python",276 "lines": 163,277 "truncated": false,278 "block": 9,279 "row": 10166280 },281 {282 "path": "Model_training/Train_embedding_model.py",283 "sha256": "f0ea867b4281c853914c786b9e8dc2bab5e78ee3efeaf02e036b2f83b38798c9",284 "language": "Python",285 "lines": 68,286 "truncated": false,287 "block": 9,288 "row": 8451289 },290 {291 "path": "Model_training/data_module.py",292 "sha256": "aad1514f680e1a25a9f67edb0bbeac99dd3916b144fc914a1eb25b11df43b4f1",293 "language": "Python",294 "lines": 118,295 "truncated": false,296 "block": 9,297 "row": 9414298 },299 {300 "path": "Model_training/datasets.py",301 "sha256": "f3a02f107c55e240071ec936115aeafd26147308cd96c9ad205e909fa378eee6",302 "language": "Python",303 "lines": 155,304 "truncated": false,305 "block": 9,306 "row": 9624307 },308 {309 "path": "Model_training/training.py",310 "sha256": "602db2516de37f919d6d8754705d60e208d103774104186b76c23663ce24310e",311 "language": "Python",312 "lines": 124,313 "truncated": false,314 "block": 9,315 "row": 9522316 },317 {318 "path": "Model_training/utils.py",319 "sha256": "dee01c0aca82642f7bc8ed0e86be794b454656c8c84a2332c8ac090fd3cac3f8",320 "language": "Python",321 "lines": 86,322 "truncated": false,323 "block": 9,324 "row": 8700325 },326 {327 "path": "README.md",328 "sha256": "e66ff98ab896c920aa1a97bdea2e0f78cfb6e3f37a8fc5dea0380fbbce6e508f",329 "language": "Text",330 "lines": 263,331 "truncated": false,332 "block": 9,333 "row": 14718334 },335 {336 "path": "Rerank/NP_score/npscorer.py",337 "sha256": "e98d6402e1f44dc56cbd181a48f47f4ff6e0c6169345df5113d2a92018c81439",338 "language": "Python",339 "lines": 129,340 "truncated": false,341 "block": 9,342 "row": 9263343 },344 {345 "path": "Rerank/features.py",346 "sha256": "1b17909014af5de9cdae542bd83b64f1c67909630058066565587882bc16c667",347 "language": "Python",348 "lines": 208,349 "truncated": false,350 "block": 9,351 "row": 10660352 },353 {354 "path": "Scripts/01_Construct_dataset.py",355 "sha256": "b0283a8466c25b26f98dc088566877c651c4051488aba40d446ff142ec6a2b5c",356 "language": "Python",357 "lines": 193,358 "truncated": false,359 "block": 9,360 "row": 10504361 },362 {363 "path": "Scripts/02_model_training.sh",364 "sha256": "26dfcd1ea9feca9d41ad5995e018a838f83141c01ad8bb97659e799790f70f2e",365 "language": "Shell",366 "lines": 10,367 "truncated": false,368 "block": 9,369 "row": 13953370 },371 {372 "path": "Scripts/03_train_rerank_model.py",373 "sha256": "0ac5710874b416ab536b32e58fa97121ccb23994b3ee63917fa54d6e6e0d0d1f",374 "language": "Python",375 "lines": 98,376 "truncated": false,377 "block": 9,378 "row": 9109379 },380 {381 "path": "Scripts/MassSpecGym/Convert.py",382 "sha256": "149ac01b5957c15b605c82b046f3506f79d75ee6c2f652a7e63c8d19cea6becb",383 "language": "Python",384 "lines": 45,385 "truncated": false,386 "block": 9,387 "row": 7582388 },389 {390 "path": "Scripts/MassSpecGym/Evaluation_denovo.sh",391 "sha256": "6aa4c73200b6e1b1ba267433228b17266ce1f4a980fa45bdad37cea9da5a905d",392 "language": "Shell",393 "lines": 14,394 "truncated": false,395 "block": 9,396 "row": 14053397 },398 {399 "path": "Scripts/MassSpecGym/Evaluation_retrieval.sh",400 "sha256": "c28797356fce6caac1893ebbfbfaa7264e56074449c740533e51975e49ad0a9e",401 "language": "Shell",402 "lines": 14,403 "truncated": false,404 "block": 9,405 "row": 14059406 },407 {408 "path": "Scripts/MassSpecGym/Prepare_dataset.py",409 "sha256": "aaaf9e66ca52bc799d155be8215a46a907c695cf32d96fbb5c29242519b8d822",410 "language": "Python",411 "lines": 43,412 "truncated": false,413 "block": 9,414 "row": 7388415 },416 {417 "path": "TemplateSearch/Embedding.py",418 "sha256": "66a2b89f7831b41af5338d06721582d46851f1424d6690420b7e44129a2c02dd",419 "language": "Python",420 "lines": 114,421 "truncated": false,422 "block": 9,423 "row": 9324424 },425 {426 "path": "TemplateSearch/QueryDB.py",427 "sha256": "27b011a1fcc90fcaf049996829ec5fc25076eea61e9984f554ab2da44e14a980",428 "language": "Python",429 "lines": 84,430 "truncated": false,431 "block": 9,432 "row": 8976433 },434 {435 "path": "run.py",436 "sha256": "454bd34e6c76c67d1e35cb5e3a5831a5a657afd9cb2c2966c0c1b1eb6056aaad",437 "language": "Python",438 "lines": 74,439 "truncated": false,440 "block": 9,441 "row": 8543442 }443 ]444}