{"id":22096248,"url":"https://github.com/aspirincode/deepfrag","last_synced_at":"2026-07-02T14:36:48.460Z","repository":{"id":92049461,"uuid":"195086580","full_name":"AspirinCode/DeepFrag","owner":"AspirinCode","description":"A pre-train and fine-tune method for predicting MS/MS spectra for a specific type of MS instrument","archived":false,"fork":false,"pushed_at":"2019-06-26T01:10:23.000Z","size":292905,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-03-24T00:56:47.998Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AspirinCode.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-07-03T16:00:08.000Z","updated_at":"2019-07-10T00:18:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"96667012-ad33-469a-859c-f5cab219b25c","html_url":"https://github.com/AspirinCode/DeepFrag","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AspirinCode/DeepFrag","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AspirinCode%2FDeepFrag","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AspirinCode%2FDeepFrag/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AspirinCode%2FDeepFrag/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AspirinCode%2FDeepFrag/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AspirinCode","download_url":"https://codeload.github.com/AspirinCode/DeepFrag/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AspirinCode%2FDeepFrag/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35051881,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-02T02:00:06.368Z","response_time":173,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-01T04:09:54.457Z","updated_at":"2026-07-02T14:36:48.425Z","avatar_url":"https://github.com/AspirinCode.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## DeepFrag\n***\nA pre-train and fine-tune method for predicting MS/MS spectra for a specific type of MS instrument.\n\n\u003cdiv align=\"center\"\u003e\n\u003cimg src=\"https://github.com/hcji/DeepFrag/blob/master/Img/Figure1A.png\" width=400 height=270 /\u003e\n\u003c/div\u003e\n\n### Depends:\n    Anaconda for python \u003e= 3.6\n    # RDKit\n    conda install -c rdkit rdkit\n    # Keras\n    conda install keras\n    # pycdk\n    pip install git+git://github.com/hcji/pycdk@master\n    # pyCFMID (optional, just used for comparing with CFM-ID)\n    pip install git+git://github.com/hcji/PyCFMID@master\n    \n### Scripts:\nAll scripts used for this work are included in the **Scripts** directory.    \n**Scripts/train_model.py** is the scrpit which is used for pre-train the model with CFM predicted spectra. The spectra are available at [MINE](http://minedatabase.mcs.anl.gov).    \n**Scripts/transfer_model_RIKEN_PlaSMA.py** is the script which is used for fine-tune the model with RIKEN PlaSMA database.    \n**Scripts/example1.py** and **Scripts/example2.py** are two examples from the test dataset.   \n**Scripts/annotation_example.py** and **Scripts/annotation_example2.py** are two examples explaining how to annotate the predicted spectra.   \n\n### Graphical Interfaces\nThis repo doesn't contain the model. One can download the whole DeepFrag at [url](https://figshare.com/articles/DeepFrag_zip/8323568). Then use the graphical interfaces with\n\n    cd ../DeepFrag\n    python DeepFragApp.py\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faspirincode%2Fdeepfrag","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faspirincode%2Fdeepfrag","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faspirincode%2Fdeepfrag/lists"}