All software
Auto-CORPus
The Automated pipeline for Consistent Outputs from Research Publications (Auto-CORPus) is a tool for the standardisation and conversion of publication HTML to three convenient machine-interpretable outputs (full-text, tables, abbreviations) in BioC-JSON formats to support biomedical text analytics.
- bioc
- html
- information retrieval
- + 4
SWMManywhere
SWMManywhere is a tool to synthesise urban drainage network models (UDMs) using publicly available data such as street network, DEM, and building footprints, across the globe. It also provides tools for generating SWMM input files and performing simulations for the synthesised UDMs.
- Algorithmic network generation
- Hydraulic modelling
- Network topology
- + 2
CoDiet-Corpus
Code repository for the creation and annotation of corpora in the CoDiet project providing scripts to generate Bronze and Silver annotated test datasets. It leverages multiple pipelines, including dictionary matching, MetaMap, enzyme annotation, PhenoBERT, MicrobELP, and BERN2.
- bionlp
- named entity recognition
- natural language processing
- + 3
MicrobELP
microbELP is a text mining pipeline for automatic recognition and normalisation of microbiome-related entities in biomedical literature. It identifies microbial mentions (excluding viruses) in full-text scientific articles and links them to their NCBI Taxonomy identifiers.
- bionlp
- entity linking
- information retrieval
- + 6
caper
The caper package for R provides a set of tools for phylogenetic comparative analyses, primary implementations of phylogenetic independent contrasts and phylogenetic generalised least squares.
evoxels
Differentiable physics framework for voxel-based microstructure simulations
- (Python)
Kaira
A PyTorch-based toolkit for simulating communication systems
- communications
- deep learning
- Python
- + 1
- (Makefile)
- (Python)
- (Shell)
Managed-File-Transfer for Prefect.IO
Extend prefect.io into a robust managed file transfer solution UI/API/programmatic creation of adhoc and cron file flows to upload and download files between servers and systems. Supports any combo of local, network, SFTP and cloud storage (thanks to rclone).
- (Dockerfile)
- (Python)
- (Shell)
ohvbd
ohvbd is an R package for retrieving (and parsing) data from a network of disease vector data sources.
- Data retrieval
- R
- vector-borne disease
- (R)
- (Rez)
- (TeX)
puzzlepiece
A GUI-forward Python framework for automating experimental setups. It focuses on abstracting communication with a piece of hardware into standard inputs, outputs, and actions, automatically generating UI components and a universal API.
- automation
- experiment automation
- experiment control
- + 3
- (Python)
pycsvy
Python reader/writer for CSV files with YAML header information
- CSV
- Inter-operability & linked data
- Python
- + 1
pzp-hardware
Laboratory hardware support Pieces for the puzzlepiece GUI & lab automation framework.
- automation
- experiment automation
- Python
- (Python)