All software
Mass Spec Studio for Clinical Proteomics
A fusion of the popular OpenMS suite of functionality with the powerful Mass Spec Studio. Users have access to OpenDIA and OpenPRM to support large scale processing of clinical proteomics data sets.
- mass spectrometry
- proteins
- proteomics
μ-awk
This is a tiny Python implementation of a line processor with Awk-like semantics. You write a set of regex-based rules. The program loops through the lines of some input file, running the matching functions on lines that match.
- python
- Text analysis & natural language processing
- (Python)
Medical Image Processing in Python
This lesson introduces some specifics of medical image processing with popular Python libraries such as SimpleITK, Pydicom and NiBabel. Reconstruction algorithms, image and DICOM anonymization, registration, segmentation, data augmentation and generative AI are covered.
- Image processing
- medical
- radiology
mibibio
Collection of microbial analysis workflows to investigate microbiological community structure, characteristics and their degradation potential.
mibiremo
MiBiReMo (Microbiome Bioremediation Reaction Module) is a Python interface to the PhreeqcRM library. The package is designed to be coupled with transport models to simulate reactive transport in porous media, with applications in environmental and geochemical engineering.
- (Makefile)
- (Python)
mibiscreen
Data handling and screening package of the Microbiome based remediation Prediction Tool
- Data Analysis
- Multi-scale & multi model simulations
- python
- ("Jupyter Notebook")
- (Python)
- (Shell)
mibitrans
A collection of analytical and semi-semianalytical solutions for hydrogeological transport phenomena
- Multi-scale & multi model simulations
- python
- (Python)
- (Shell)
Mimetic Operators Library Enhanced (MOLE)
MOLE is a high-quality (C++ & MATLAB/Octave) library of high-order mimetic operators to solve partial differential equations. It provides discrete analogs of vector calculus operators: Gradient, Divergence, Laplacian, Bilaplacian, and Curl. These operators satisfy local and global conservation laws.
- Mathematical Software
- Mimetic Operators
- Partial differential equations
- (C)
- (C++)
- (CMake)
- + 3
minimism
A minimal distributed MPI port from UFEMISM, used as a basis for UFEMISM2.0
- Finite volume method
- ice sheet
- MPI
- + 1
- (Fortran)
- (Makefile)
- (Mathematica)
- + 4
MINTED
MINTED (Making Identifiers Necessary for Tracking Evolving Data) aims to apply dataset citation Digital Object Identifiers (DOIs) and researcher ORCIDs into ONC's Oceans 3.0 digital infrastructure.
- oceanography
- Oceans
- persistent identifiers
Mixed Meal Model SBML
This software generates the SBML version of the Mixed Meal Model, for predicting the glucose level evolution after the intake of a meal.
- Digital Twins
- modelling
- (Python)
- (Shell)
mkdocs rich argparse
An MkDocs plugin to generate documentation for a rich argparse parser. It renders commands, sub commands and sub-sub commands which can have rich help messages.
- python
- (Python)
ModuleMixins.jl
Make your Julia modules composable! With ModuleMixins you can design larger programs in Julia, building out components by merging structure definitions from smaller components, similar to designing an [Entity Component System](https://en.wikipedia.org/wiki/Entity_component_system).
- Entity Component System
- Julia Package
- Metaprogramming
- + 2
- (Julia)
MorphoDynamX
An integrated image processing and simulation platform
MorphoMechanX
FEM simulation add-on for MorphoDynamX
MPET
This software is designed to run simulations of batteries with porous electrodes using porous electrode theory, which is a volume-averaged, multiscale approach to capture the coupled behavior of electrolyte and active material within electrodes
- (Dockerfile)
- (Python)
MSS-IMProv
An Integrative Modeling Platform
- mass spectrometry
- Modeling
- proteins
NanopubJL
JupyterLab extension to aid in searching and publishing of Nanopublications in a python notebook
- Inter-operability & linked data
- (CSS)
- (Dockerfile)
- (JavaScript)
- + 3
Nature Counts
The NatureCounts platform allows users to collect, archive, interpret and access wildlife data to advance the understanding of bird populations across the Western Hemisphere.
- bird monitoring
- conservation science
- open data
- (CSS)
- (R)
nedextract
nedextract is a python library that helps you to extract information on person names and organisations mentioned in Dutch (annual report) PDF files.
- ("Jupyter Notebook")
- (Python)
- (Shell)
NetCDF2LittleR
An application to convert NetCDF files to the Little-R format
- (CMake)
- (Fortran)
- (Pascal)
NeuroAnalyzer
NeuroAnalyzer is a Julia toolbox for analyzing neurophysiological data.
- EEG
- fNIRS
- MEG
- + 2
NeuroGym
NeuroGym is a curated collection of neuroscience tasks with a common interface. The goal is to facilitate the training of neural network models on neuroscience tasks.
- deep learning
- Machine learning
- Neuroscience
- + 3
- (Python)
NPLinker eScience Workshop GenMetMine Materials
These materials were used as a part of the NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinformatics/teaching/nplinker_workshop.htm Most materials are available in a format facilitating its reuse.
- Data mining
- genomics
- Inter-operability & linked data
- + 4
Nunaliit
The Nunaliit Atlas Framework aims to make it easy to tell stories and highlight relationships between many different forms of information from a variety of sources, using maps as a central way to connect and interact with the data.
- atlas
- cartography
- database
- + 6
- (C)
- (CSS)
- ("Go Template")
- + 10
OBiBa Agate
Agate is a web application that offers users related services to the OBiBa software stack.
- authentication
- Epidemiology
- (Batchfile)
- (FreeMarker)
- (HTML)
- + 7
OBiBa Mica
Mica is OBiBa's software application that is used to create data web portals for large-scale epidemiological studies or multiple-study consortia.
- euCanSHare, software integration
- (Batchfile)
- (CSS)
- (FreeMarker)
- + 7
OBiBa Opal
Opal is OBiBa's core data repository application for epidemiological studies.
- euCanSHare, software integration
- (ANTLR)
- (Batchfile)
- (HTML)
- + 8
Ocean Networks Canada
By bringing data to the surface, ONC provides ocean intelligence to scientists, governments, organizations, and citizens. Ocean data are archived, processed and made freely available via ONC’s data management system, Oceans 3.0.
OCTSEG
Analyze retinal optical coherence tomography images.
- Image processing
- (M)
- (MATLAB)
One button compute
Web application for running a CWL workflow on a bunch of files.
- Optimized data handling
- Workflow technologies
- ("Common Workflow Language")
- (HTML)
- (Python)
OpenDA
Open data assimilation toolbox. OpenDA is an open interface standard for a set of tools to quickly implement data-assimilation and calibration for arbitrary numerical models.
- Optimized data handling
- (Batchfile)
- (Brainfuck)
- (C)
- + 23
Open Matrices Stimulus Set (omss)
omss is a Python package for generating matrix reasoning puzzles, inspired by Raven's Progressive Matrices. It allows users to generate an unlimited number of customizable puzzles across a range of difficulty levels by setting rules for visual elements.
- Intelligence
- Matrices
- python
- + 1
- (Python)
OpenRefine
OpenRefine is a powerful free, open source tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.
- Data Analysis
- Data Science
- (Batchfile)
- (CSS)
- (HTML)
- + 8
OpenSim Creator
A UI for building OpenSim models
- biomechanical engineering
- opensim
- Simulation
- (AppleScript)
- (Batchfile)
- (C)
- + 5
Orange3 Argument Mining Add-on
This open-source Python package facilitates the processing, analysis, and visualization of argument corpora. Additionally, It offers user-friendly GUIs integrated into the Orange3 scientific workflow platform, enabling non-programmers to utilize its capabilities.
- Argument mining
- Natural Language Processing
- python
- + 1
- (Python)
Orange3 Story Navigator
Add-on providing quantitative textual story analysis based on principles in narrative psychology
- narrative psychology
- orange3
- text analysis
- (Python)
Orange Hackathon
Orange modules for text processing in the project What Works When for Whom
- (CSS)
- ("Jupyter Notebook")
- (Python)
- + 2
Osmium
Start, stop and monitor applications remotely via a HTTP interface.
- High performance computing
- ("API Blueprint")
- (Java)
oTree Demo Experiments
oTree demo experiment: Public goods game
- behavioral research
- oTree
- Workflow technologies
- (HTML)
- (JavaScript)
- (Procfile)
- + 1
oTree Development Environment
A Docker environment for programming against multiple oTree server
- oTree
- (Dockerfile)
- (Makefile)
- (Shell)
oTree Waiting Room
A load balancer for oTree servers.
- oTree
- (HTML)
- (JavaScript)
- (Shell)
Overture Arranger
Data can be messy, let Arranger organize it for you.
- (CSS)
- (HTML)
- (JavaScript)
- + 3
Overture Data Management System
Overture is a collection of open-source, extendable solutions for big-data genomic science that research institutions and individual researchers can use to support their work.
- authentication
- cloud storage
- genomics
- + 2
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Ego
A stateless authorization and user management service.
- Data Indexing
- Elasticsearch Automation
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Maestro
Organizing your distributed data into one index.
- Data Indexing
- Elasticsearch Automation
- (Dockerfile)
- (Groovy)
- (Java)
- + 1
Overture Score
Transfer data quickly and easily to and from any cloud-based storage system.
- Cancer Genomics
- Cloud Storage & Transfer
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Song
Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.
- Cancer Genomics
- Metadata Management
- Metadata Validation
- (Batchfile)
- (Dockerfile)
- (Go)
- + 7