[38;5;12m                                                                         [39m[38;2;255;187;0m[1m[4mAwesome Computational Biology [0m[38;5;14m[1m[4m![0m[38;2;255;187;0m[1m[4mAwesome[0m[38;5;14m[1m[4m (https://awesome.re/badge.svg)[0m[38;2;255;187;0m[1m[4m (https://awesome.re)[0m

[38;5;12mA knowledge collection of databases, software and papers related to computational biology.[39m

[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mComputational biology involves the development and application of data-analytical and theoretical methods,[39m
[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mmathematical modelling and computational simulation techniques to the study of biological, ecological,[39m
[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mbehavioural, and social systems. - [39m[38;5;14m[1mWikipedia[0m[38;5;12m (https://en.wikipedia.org/wiki/Computational_biology)[39m

[38;2;255;187;0m[4mContents[0m

[38;5;12m- [39m[38;5;14m[1mDatabases[0m[38;5;12m (#databases)[39m
[38;5;12m  - [39m[38;5;14m[1mscRNA[0m[38;5;12m (#scrna)[39m
[38;5;12m  - [39m[38;5;14m[1mCompound[0m[38;5;12m (#compound)[39m
[38;5;12m  - [39m[38;5;14m[1mPathway[0m[38;5;12m (#pathway)[39m
[38;5;12m  - [39m[38;5;14m[1mMass Spectra[0m[38;5;12m (#mass-spectra)[39m
[38;5;12m  - [39m[38;5;14m[1mProtein[0m[38;5;12m (#protein)[39m
[38;5;12m  - [39m[38;5;14m[1mGenome[0m[38;5;12m (#genome)[39m
[38;5;12m  - [39m[38;5;14m[1mDisease[0m[38;5;12m (#disease)[39m
[38;5;12m  - [39m[38;5;14m[1mInteraction[0m[38;5;12m (#interaction)[39m
[38;5;12m- [39m[38;5;14m[1mPreprocess[0m[38;5;12m (#preprocess)[39m
[38;5;12m- [39m[38;5;14m[1mMachine Learning Tasks and Models[0m[38;5;12m (#machine-learning-tasks-and-models)[39m
[38;5;12m  - [39m[38;5;14m[1mDrug Repurposing[0m[38;5;12m (#drug-repurposing)[39m
[38;5;12m  - [39m[38;5;14m[1mDrug Target Interaction[0m[38;5;12m (#drug-target-interaction)[39m
[38;5;12m  - [39m[38;5;14m[1mCompound Protein Interaction[0m[38;5;12m (#compound-protein-interaction)[39m
[38;5;12m  - [39m[38;5;14m[1mPre-trained embedding[0m[38;5;12m (#pre-trained-embedding)[39m
[38;5;12m  - [39m[38;5;14m[1mLLM for biology[0m[38;5;12m (#llm-for-biology)[39m

[38;2;255;187;0m[4mDatabases[0m
[38;2;255;187;0m[4mscRNA[0m
[38;5;12m- [39m[38;5;14m[1mGene Expression Omnibus[0m[38;5;12m (https://www.ncbi.nlm.nih.gov/geo/) - Public functional genemics database.[39m
[38;5;12m- [39m[38;5;14m[1mSingle Cell PORTAL[0m[38;5;12m (https://singlecell.broadinstitute.org/single_cell) - Public database for single cell RNA.[39m
[38;5;12m- [39m[38;5;14m[1mSingle Cell Expression Atlas[0m[38;5;12m (https://www.ebi.ac.uk/gxa/sc/home) - Public database for single cell RNA.[39m
[38;2;255;187;0m[4mCompound[0m
[38;5;12m- [39m[38;5;14m[1mPubChem[0m[38;5;12m (https://pubchem.ncbi.nlm.nih.gov/) - One of the biggest chemical database such as compounds, genes and proteins.[39m
[38;5;12m- [39m[38;5;14m[1mChEBI[0m[38;5;12m (https://www.ebi.ac.uk/chebi/) - Chemical database  focused on small chemical compounds.[39m
[38;5;12m- [39m[38;5;14m[1mChEMBL[0m[38;5;12m (https://www.ebi.ac.uk/chembl/) - Database of bioactive molecules with drug-like properties.[39m
[38;5;12m- [39m[38;5;14m[1mChemSpider[0m[38;5;12m (http://www.chemspider.com/) - Chemical structure database.[39m
[38;5;12m- [39m[38;5;14m[1mKEGG COMPOUND[0m[38;5;12m (https://www.genome.jp/kegg/compound/) - Collection of small molecules and biopolymers.[39m
[38;5;12m- [39m[38;5;14m[1mLIPID MAPS[0m[38;5;12m (https://www.lipidmaps.org/databases/lmsd/overview) - Database of lipids.[39m
[38;5;12m- [39m[38;5;14m[1mRhea[0m[38;5;12m (https://www.rhea-db.org/) - Database of chemical reactions.[39m
[38;5;12m- [39m[38;5;14m[1mDrug Repurposing Hub[0m[38;5;12m (https://repo-hub.broadinstitute.org/repurposing#download-data) - Collections of drug repurposing data containing drug, moa, target etc.[39m
[38;2;255;187;0m[4mPathway[0m
[38;5;12m- [39m[38;5;14m[1mPathwayCommons[0m[38;5;12m (https://www.pathwaycommons.org/) - Database of Pathways and Interactions.[39m
[38;5;12m- [39m[38;5;14m[1mKEGG PATHWAY[0m[38;5;12m (https://www.genome.jp/kegg/pathway.html) - Collection fo drawn pathway maps.[39m
[38;5;12m- [39m[38;5;14m[1mWikiPathways[0m[38;5;12m (https://wikipathways.org/) - Database of biological pathways.[39m
[38;2;255;187;0m[4mMass Spectra[0m
[38;5;12m- [39m[38;5;14m[1mMassBank[0m[38;5;12m (http://www.massbank.jp/) - Open souce databases and tools for mass spectrometry reference spectra.[39m
[38;5;12m- [39m[38;5;14m[1mMoNA MassBank of North America[0m[38;5;12m (https://mona.fiehnlab.ucdavis.edu/) - Meta database of metabolite mass spectra, metadata and associated compounds.[39m
[38;2;255;187;0m[4mProtein[0m
[38;5;12m- [39m[38;5;14m[1mTHE HUMAN PROTEIN ATLAS[0m[38;5;12m (https://www.proteinatlas.org/) - One of the biggest human protein database contained cells, tissues, and organs. [39m
[38;5;12m- [39m[38;5;14m[1mPROTEIN DATA BANK[0m[38;5;12m (https://www.rcsb.org/) - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.[39m
[38;5;12m- [39m[38;5;14m[1mUniProt[0m[38;5;12m (https://www.uniprot.org/) - The collection of functional information on proteins.[39m
[38;5;12m- [39m[38;5;14m[1mAlphaFold Protein Structure Database[0m[38;5;12m (https://alphafold.ebi.ac.uk/api-docs) - Database of 3D protein structures.[39m
[38;2;255;187;0m[4mGenome[0m
[38;5;12m- [39m[38;5;14m[1mHuman Genome Resources at NCBI[0m[38;5;12m (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml) - Database of image, proteomics, transcriptomics and systems biology.[39m
[38;5;12m- [39m[38;5;14m[1mGenBank[0m[38;5;12m (https://www.ncbi.nlm.nih.gov/genbank/) - Database of genetic sequence offered by NCBI.[39m
[38;5;12m- [39m[38;5;14m[1mUCSC Genome Browser[0m[38;5;12m (https://genome.ucsc.edu/) - Genome blowser offered by UCSC.[39m
[38;5;12m- [39m[38;5;14m[1mcBioPortal[0m[38;5;12m (https://www.cbioportal.org/) - Database of Cancer Genomics. This has overall metaview for a lot of patients.[39m
[38;2;255;187;0m[4mDisease[0m
[38;5;12m- [39m[38;5;14m[1mKEGG DRUG[0m[38;5;12m (https://www.genome.jp/kegg/drug/) - Comprehensive drug information resource for approved drugs.[39m
[38;5;12m- [39m[38;5;14m[1mDrugBank[0m[38;5;12m (https://www.drugbank.com/) - A database of drug and target maintained by the University of Alberta.[39m
[38;2;255;187;0m[4mInteraction[0m
[38;5;12m- Drug Gene Interaction[39m
[38;5;12m  - [39m[38;5;14m[1mDGIdb[0m[38;5;12m (https://www.dgidb.org/) - A database of drug-gene interactions and the druggable genome.[39m
[38;5;12m  - [39m[38;5;14m[1mComparative Toxicogenomics Database[0m[38;5;12m (http://ctdbase.org/) - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.[39m
[38;5;12m  - [39m[38;5;14m[1mSNAP[0m[38;5;12m (https://snap.stanford.edu/biodata/datasets/10002/10002-ChG-Miner.html#:~:text=Dataset%20information,or%20activation%20of%20the%20drug.) - A dataset which contains Drug-gene interactions. [39m
[38;5;12m  - [39m[38;5;14m[1mComparative Toxicogenomics Database[0m[38;5;12m (https://ctdbase.org/) - A database for drug-target interactions.[39m
[38;5;12m  - [39m[38;5;14m[1mTherapeutics Data Commons[0m[38;5;12m (https://tdcommons.ai/) - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.[39m
[38;5;12m- Drug (-Cell line) Response[39m
[38;5;12m  - [39m[38;5;14m[1mNCI60[0m[38;5;12m (https://dtp.cancer.gov/discovery_development/nci-60/) A database which focus on 60 cancer cell lines with many drugs.[39m
[38;5;12m  - [39m[38;5;14m[1mGenomics of Drug Sensitivity in Cancer (GDSC)[0m[38;5;12m (https://www.cancerrxgene.org/) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.[39m
[38;5;12m  - [39m[38;5;14m[1mCancer Cell Line Encyclopedia[0m[38;5;12m (https://sites.broadinstitute.org/ccle/) - A database of cancer cell lines. This has 1000 cell lines.[39m
[38;5;12m- Chemical Protein Interaction[39m
[38;5;12m  - [39m[38;5;14m[1mSTITCH[0m[38;5;12m (http://stitch.embl.de/) - A database of Chemical Protein Interaction.[39m
[38;5;12m  - [39m[38;5;14m[1mBindingDB[0m[38;5;12m (https://www.bindingdb.org/rwd/bind/index.jsp) - A database of compounds and targes.[39m
[38;5;12m- Protein-Protein Interaction[39m
[38;5;12m  - [39m[38;5;14m[1mSTRING[0m[38;5;12m (https://string-db.org/) - Protein-Protein Interaction Networks for several organisms.[39m
[38;5;12m  - [39m[38;5;14m[1mBioGRID[0m[38;5;12m (https://thebiogrid.org/) - Database of Protein, Genetic and Chemical Interactions.[39m
[38;5;12m  - [39m[38;5;14m[1mHIPPIE[0m[38;5;12m (http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/) - Human Protein-Protein Interaction database.[39m

[38;2;255;187;0m[4mPreprocess[0m

[38;5;12m- [39m[38;5;14m[1mChemistry Development Kit[0m[38;5;12m (https://github.com/cdk/cdk) - A software of cheminformatics and Machine Learning.[39m
[38;5;12m- [39m[38;5;14m[1mRDKit[0m[38;5;12m (https://github.com/rdkit/rdkit) - A software of cheminformatics and Machine Learning.[39m
[38;5;12m- [39m[38;5;14m[1mScanpy[0m[38;5;12m (https://scanpy.readthedocs.io/en/stable/) - scRNA analysis library in Python.[39m
[38;5;12m- [39m[38;5;14m[1mSeurat[0m[38;5;12m (https://satijalab.org/seurat/) - scRNA analysis library in R.[39m

[38;2;255;187;0m[4mMachine Learning Tasks and Models[0m

[38;2;255;187;0m[4mDrug Repurposing[0m

[38;5;12m- [39m[38;5;14m[1mDeepPurpose[0m[38;5;12m (https://github.com/kexinhuang12345/DeepPurpose) - A DL Library for Drug Repurposing and so on. [39m
[38;5;12m- [39m[38;5;14m[1mDRKG[0m[38;5;12m (https://github.com/gnn4dr/DRKG) - A library for biological knowledge graph.[39m

[38;2;255;187;0m[4mDrug Target Interaction[0m

[38;5;12m- [39m[38;5;14m[1mNeoDTI[0m[38;5;12m (https://github.com/FangpingWan/NeoDTI) - A library for Drug Target Interaction.[39m

[38;2;255;187;0m[4mCompound Protein Interaction[0m

[38;5;12m- [39m[38;5;14m[1mMCPINN[0m[38;5;12m (https://github.com/mhlee0903/multi_channels_PINN) - A library for drug discovery using Compound Protein Interaction and Machine Learning.[39m
[38;5;12m- [39m[38;5;14m[1mTransformerCPI[0m[38;5;12m (https://github.com/lifanchen-simm/transformerCPI) - A library for Compound Protein Interaction prediction using Transformer.[39m

[38;2;255;187;0m[4mPre-trained embedding[0m

[38;5;12m- [39m[38;5;14m[1mEvolutionary Scale Modeling[0m[38;5;12m (https://github.com/facebookresearch/esm) - a library for protein embeddings.[39m
[38;5;12m- [39m[38;5;14m[1mChemBERTa-2[0m[38;5;12m (https://github.com/seyonechithrananda/bert-loves-chemistry) - a library for chemical embeddingg and prediction.[39m

[38;2;255;187;0m[4mLLM for biology[0m

[38;5;12m- [39m[38;5;14m[1mAI4Chem/ChemLLM-7B-Chat[0m[38;5;12m (https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) - LLM for chemical and molecule science[39m
[38;5;12m- [39m[38;5;14m[1mBioGPT[0m[38;5;12m (https://github.com/microsoft/BioGPT) - LLM for Biomedical text generation[39m



