Add ProtGPT2, RFdiffusion, and ProteinMPNN projects #23
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vasimuddin
approved these changes
Nov 27, 2024
sanchit-misra
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Dec 13, 2024
* Autodock (#14) * Added Autodock workload * removed unnecessary contents * removed unnecessary contents * Removed old files and updated README and data download script * updated readme and data download script * updated readme and data download script * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated data download script for the test cases --------- Co-authored-by: arunvelliyangiri18 <[email protected]> * Autodock vina (#15) * Added Autodock workload * Added Autodock-Vina workload * removed unnecessary contents * removed unnecessary contents * removed unnecessary contents * removed unnecessary contents * removed Autodock * added data download script and removed 5wlo * Added updated README * updated README and data download script * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated data download script for the test cases * updated README * updated README --------- Co-authored-by: arunvelliyangiri18 <[email protected]> * Added ESM (#13) * add esm docker files and patch files * add esm docker files and patch files * add esm docker files and patch files * add esm docker files and patch files --------- * added STAR aligner (v2.7.11b) as a submodule in applications (#17) * Add ProtGPT2, RFdiffusion, and ProteinMPNN projects (#23) * adding protgpt2 * adding ProteinMPNN * adding RFdiffusion * update protgpt2.py file and README * update ProteinMPNN Dockerfile * In this commit, I have update the Dockerfile, RFdiffusion patch, symmetry file, and run_inference file. * Updated the Open Omics block diagram (#20) * Updated the Open Omics block diagram * Updated the block diagram * Update README.md to reflect 3.0 release * Uploaded the new Open Omics diagram for v3.0 * Update README.md * Updated the Open Omics diagram with better quality * Update path to Open Omics diagram * removed rfd, proteinmpnn, protgpt, will send the pr again * cleanup the files for Rfdiffusion and ProteinMPNN and Protgpt2 (#24) * adding protgpt2 * adding ProteinMPNN * adding RFdiffusion * update protgpt2.py file and README * update ProteinMPNN Dockerfile * In this commit, I have update the Dockerfile, RFdiffusion patch, symmetry file, and run_inference file. * removed RFdiffusion optimize code * removed ProteinMPNN optimize code * Update README.md * Update README.md * Update README.md * Update README.md * cleanup hidden files * cleanedup some stray hidden files * Added privacy notice (#16) (#19) Co-authored-by: sanchit-misra <[email protected]> * Autodock (#21) * Added Autodock workload * removed unnecessary contents * removed unnecessary contents * Removed old files and updated README and data download script * updated readme and data download script * updated readme and data download script * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated data download script for the test cases * updated README for proxy build command for docker --------- Co-authored-by: arunvelliyangiri18 <[email protected]> Co-authored-by: manasi-t24 <[email protected]> * Autodock vina (#22) * Added Autodock workload * Added Autodock-Vina workload * removed unnecessary contents * removed unnecessary contents * removed unnecessary contents * removed unnecessary contents * removed Autodock * added data download script and removed 5wlo * Added updated README * updated README and data download script * updated README * updated README * updated README * updated README * updated README * updated README * updated README * updated data download script for the test cases * updated README * updated README * updated README for proxy build command for docker --------- Co-authored-by: arunvelliyangiri18 <[email protected]> Co-authored-by: manasi-t24 <[email protected]> * updated ProteinMPNN and ProtGPT2 and RFdiffusion Dockerfiles (#28) * ESM: Dockerfiles updated to work independently (#26) * Add ESM changes * Add ESM changes * MoFlow workload added (#18) * Added privacy notice (#16) * Add MoFlow updates * Add MoFlow updates * Add MoFlow updates --------- Co-authored-by: sanchit-misra <[email protected]> * Update README.md (#29) * Updated ESM README changes (#31) Corrected LM design command line * Adding multimer support to v3.0-release branch (#33) * Adding support for AlphaFold2 Multimer * single docker files for handling monomer and multimer cases * changing to the main branch of open-omics-alphafold * Added privacy notice (#16) (#25) * removed the commented code --------- Co-authored-by: sanchit-misra <[email protected]> * git clone replaced with wget for release code (#34) * Update README.md to reflect v3.0 additions (#35) * fixed wget OO downloads urls in fq2bam and dv1 dockers for V3.0 release (#36) * updated docker files (fq2bam, dv1) with git download * Update README.md * Update README.md * clean up * clean up dockers --------- Co-authored-by: vasimuddin.md <[email protected]> Co-authored-by: vasimuddin.md <[email protected]> --------- Co-authored-by: sri480673 <[email protected]> Co-authored-by: arunvelliyangiri18 <[email protected]> Co-authored-by: Vasimuddin Md <[email protected]> Co-authored-by: Rahamathullah365 <[email protected]> Co-authored-by: sanchit-misra <[email protected]> Co-authored-by: Chirayu Haryan <[email protected]> Co-authored-by: manasi-t24 <[email protected]> Co-authored-by: Narendra Chaudhary <[email protected]> Co-authored-by: vasimuddin.md <[email protected]> Co-authored-by: vasimuddin.md <[email protected]>
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This pull request adds support for the following projects: