All software
LUE
LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.
- Agent-based modeling
- environmental modelling
- field based modelling
- + 6
- (Batchfile)
- (C)
- (C++)
- + 6
microGWAS
microGWAS is a snakemake-powered pipeline to carry out an end-to-end microbial GWAS analysis. Starting from genome assemblies and a phenotype file, microGWAS will run a number of associations using pyseer, annotate the associations results, and generating a number of functional enrichment tests.
- GWAS
- mGWAS
- Pipeline
- + 2
- Python
- Shell
- R
MyCoRe
MyCoRe (acronym for My Content Repository) is an open source repository software framework for building disciplinary or institutional repositories, digital archives, digital libraries, and scientific journals.
- CMS
- digital archive
- digital library
- + 3
- Java
- TypeScript
- XSLT
- + 7
Noodles
Task-based parallel programming model in Python that offers the same intuitive interface when running complex workflows on your laptop or on large computer clusters.
- High performance computing
- Workflow technologies
- (HTML)
- ("Jupyter Notebook")
- (Lua)
- + 2
Hercules
Retrieve recent tweets from certain users and classify them with machine learning
- Machine learning
- Text analysis & natural language processing
- ("Jupyter Notebook")
- (Python)
- (Shell)
SicHash
A perfect hash function is a function that has no collisions on a given set. SicHash places objects in a cuckoo hash table and then stores the final hash function choice of each object in a retrieval data structure. Using irregular cuckoo hashing, each object has a different number of hash functions
- C++
- TeX
- Shell
- + 2
stream2segment
A Python library and command line application to download, process and visualize event-based seismic waveform segments, specifically designed to manage big volumes of data
- Big data
- data managment
- Data Visualization
- + 5
- Python
- Jupyter Notebook
- HTML
- + 1
TomoBEAR
TomoBEAR is an open-source configurable and customizable modular pipeline for streamlined and parallelized processing of large-scale cryo-electron tomography data for subtomogram averaging.
- Alignment
- automated reasoning
- cluster
- + 16
- MATLAB
- M
- Python
- + 1
WEARDA
WEARDA: recording wearable sensor data for human activity monitoring.
- embedded software
- GPS
- Human activity monitoring
- + 4
- (C)
- (TeX)
Xenon gRPC server
Run applications remotely via a gRPC interface.
- High performance computing
- (Java)
13CFLUX
13CFLUX - third-generation, high-performance simulation engine for isotopically stationary and non-stationary 13C metabolic flux analysis within an open, extensible software ecosystem.
- Biotechnology
- Fluxomics
- Isotope labeling
- + 6
- C++
- Python
- CMake
- + 2
Network structures
A draft model with some useful code for creating different network structures using the Netlogo NW extension: small-world, preferential attachment, circular, star, wheel, lattice, random, nearest neighbours.