justaddcoffee
Bioinformatics, computational biology, graphs, ML, AI, data science, coffee
Lawrence Berkeley National LabBerkeley, CA
Pinned Repositories
kgx
KGX is a Python library for exchanging Knowledge Graphs
berkeleybop.github.io
Homepages for the Berkeley BOP.
go-cam-models-kg-covid-19
GO-CAM models to be ingested into kg-covid-19
justaddcoffee-chembl_antiviral_smile_and_embeddings
kg-covid-19-node2vec
Apply N2V to kg-covid-19 knowledge graph
npc_plos_one_12_2013
NPC PLOS One paper
upheno_node2vec
kg-covid-19
An instance of KG Hub to produce a knowledge graph for COVID-19 response.
embiggen
🍇 Embiggen is the Python Graph Representation learning, Prediction and Evaluation submodule of the GRAPE library.
SLDBGen
justaddcoffee's Repositories
justaddcoffee/berkeleybop.github.io
Homepages for the Berkeley BOP.
justaddcoffee/go-cam-models-kg-covid-19
GO-CAM models to be ingested into kg-covid-19
justaddcoffee/justaddcoffee-chembl_antiviral_smile_and_embeddings
justaddcoffee/area1_target_info
Protein Target Information for Area 1
justaddcoffee/curate-gpt
LLM-driven curation assist tool (pre-alpha)
justaddcoffee/dans_kg_idg
Exp using DANS on KG-IDG
justaddcoffee/embed_monarch
Make embeddings of the Monarch Knowledge Graph
justaddcoffee/embed_pubmed
Embeddings of pubmed
justaddcoffee/ensmallen_experiments
Experiments on the EnsmallenGraph library.
justaddcoffee/ensmallen_graph
Rust library to run weighted random walks on very big graphs.
justaddcoffee/ga_pyphetools_cohorts
justaddcoffee/gcloud_storage_read_write
justaddcoffee/geneontology.github.io
Repository for storing GO documentation, directly available through the general GO site
justaddcoffee/kg-covid-19
An instance of KG Hub to produce a knowledge graph for COVID-19 response.
justaddcoffee/kg-hub-viz
Some hacking on visualization of KG-Hub summary stats
justaddcoffee/kg_covid_19_drug_analyses
justaddcoffee/kg_covid_19_high_mem_issue
justaddcoffee/load_go_in_ensmallen_graph
justaddcoffee/madam_curie
Utility to convert CURIEs to URLs
justaddcoffee/make_latex_table1
justaddcoffee/oakx-grape
Experimental OAK plugin for Grape
justaddcoffee/ontogpt
GPT-based ontological extraction tools, including SPIRES
justaddcoffee/phenopacket-tools
Java CLI and library for creating, converting and validating GA4GH Phenopackets
justaddcoffee/phenotype2phenopacket
justaddcoffee/pheval.exomiser
Exomiser plugin for PhEval.
justaddcoffee/plot_phenogpt_plots
justaddcoffee/rustsim
A fork of rustsim to investigate adding phenomizer and possibly genetic algorithm-type things
justaddcoffee/semsimian-server
Rust web server for Semsimian - a semantic similarity implementation
justaddcoffee/tensorflow_rocm_docker
The files I use to run tensorflow inside of a docker on a machine with AMD gpus
justaddcoffee/venomx
Vector Embedding Named Object Model indeX