afg1

Bioinformatician @RNAcentral, part of EMBL-EBI in Cambridge, UK. Formerly part of @rrr-uom-projects

Pinned Repositories

cad2gdml
Simple program using CADMesh and Geant4 to export a GDML file from a CAD file (e.g. STL)
Language:C++10
DataClassifier
Quick and dirty script to enable manual classification of images. Requires PyQt5
Language:Python21
keyboard
Language:Python00
RadNetAIDemo
Notebook for the radnet AI live coding session
Language:Jupyter Notebook41
seq-feat
Sequence features in Rust!
Language:Rust00
SOBPtools
A couple of python scripts I wrote to produce spread out bragg peak profiles in 2D (i.e. depth-dose curves)
Language:Python41
trismus-atlas
A trismus related OAR atlas, developed by Dr Christina Hague, code by me. Rehosted here because UoM version is offline
Language:JavaScript30
rnacentral-import-pipeline
RNAcentral data import pipeline
Language:Python2 5 840
rnacentral-webcode
RNAcentral website source code
Language:Python30 5 4419
FLARE21
https://flare.grand-challenge.org/FLARE21/
Language:Python20

afg1's Repositories

afg1/RadNetAIDemo
Notebook for the radnet AI live coding session
Language:Jupyter Notebook41
afg1/pride-chatbot
Language:Python1
afg1/seq-feat
Sequence features in Rust!
Language:Rust00
afg1/ARISE
afg1/ARISE_feature_extraction
Small repo for the feature extraction code used in standard clustering
Language:Python
afg1/augmentoolkit
Convert Compute And Books Into Instruct-Tuning Datasets
Language:Python
afg1/AutoAWQ
AutoAWQ implements the AWQ algorithm for 4-bit quantization with a 2x speedup during inference. Documentation:
afg1/CPC2
Dockerising CPC2 for simplified use
Language:Dockerfile
afg1/DigitalHealthPG
Language:Jupyter Notebook
afg1/epmc-xml
Language:Python
afg1/fastembed
Fast, Accurate, Lightweight Python library to make State of the Art Embedding
Language:Jupyter Notebook
afg1/go_def_scoring
Language:Python
afg1/jats-parser
python scripts parsing the Europe PMC interchange format JATS using the lxml library
Language:Python
afg1/langchain
⚡ Building applications with LLMs through composability ⚡
afg1/litsumm-2
Improved version of LitSumm with better information extraction
Language:Python
afg1/llama-cpp-python
Python bindings for llama.cpp
Language:Python
afg1/llama.cpp
Port of Facebook's LLaMA model in C/C++
Language:C
afg1/mindsdb
The platform for customizing AI from enterprise data
afg1/pi_calc
Language:Rust
afg1/progressive_build
Fast gene finder for expression atlas
Language:Rust
afg1/prometheus2-litsumm-eval
Language:Python
afg1/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Language:Python
afg1/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
Language:C
afg1/rna-lang-model
Try to make a language model for RNA!
Language:Python
afg1/rna-type-model
Language:Python
afg1/rnacentral-new-db-import
Code to create the needed tables and other changes in the RNAcentral database for new imports
Language:Mustache
afg1/timesheet
CLI thing to add entries to timesheet
Language:Python
afg1/uniprot-demos
Language:Python
afg1/whisper.cpp
Port of OpenAI's Whisper model in C/C++
afg1/whispercpp.py
Python bindings for whisper.cpp