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For initial assessment of the best strategy of migrating OmniPath to BioCypher, we will build a pipeline with secondary adapter and create a representative schema of the OmniPath KG to be developed. D…
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Opened issue to list here other Python libraries to be checked.
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### **Introduction and background**
The problem presented in this paper deals with a primary focus in systems biology; mainly, the identification of a networks reactions that yield a set of pathways …
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# pera
Automated extraction of prior information from signaling databases.
Pathway Extraction and Reduction Algorithm (PERA) was developed to automatically extract prior information from multiple s…
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Currently, the [gromit](https://github.com/MD-Studio/cerise-mdstudio-das5/blob/develop/mdstudio/gromit/gromit_mpi.sh) script accept as input the protein and ligand coordinates and topology, together w…
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Thanks in part to @mellybelly @kltm @lwinfree and all the reusable data team, StringDB is now all cc-by, so we can pull a lot more data. Currently we are only ingesting the protein.links.detailed fil…
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Hi, recently I buy lot of memory to do bigger structure interactions, and I have the impression Alpha Pulldown cannot take more than 10 proteins (here 20). Maybe it's cause the name is too long ?
T…
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I'm trying to calculate ligand-aminoacid interaction from OpenMM simulation from pdb topology and xtc trajectory. Ligand structure is show below
![image](https://github.com/chemosim-lab/ProLIF/assets…
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Documentation to setting up instances of KG on AWS: https://github.com/clinical-biomarkers/biomarker-partnership/tree/main/supplementary_files/documentation
Goal: Create knowledge graphs and cyph…
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"Docking" used to be a Topic (EDAM 1.12) but was deprecated, and merged into the notion of [Molecular modeling](http://edamontology.org/topic_2275). Yet it's suggested as a topic in https://github.co…