All software
QUAST
QUAST is a state-of-the-art tool for (meta)genome assembly evaluation, computing over 50 quality metrics and presenting results in plain text, static plots, and interactive HTML reports.
- Data Visualization
- FAIR Software
- Genome assembly
- + 4
- AMPL
- C++
- Python
- + 12
ComplexHeatmap
Complex heatmaps are efficient in visualizing associations between different sources of data sets and revealing potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
- bioconductor
- Clustering
- Data Science
- + 3
- R
- CSS
haddock3
Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a modular software for for the integrative modeling and refinement of biomolecular complexes.
- biomolecular complexes
- docking
- energetics
- + 4
- Python
- Fortran
- Jupyter Notebook
- + 11
maftools
maftools is a comprehensive toolkit for processing somatic variants from cohort-based cancer genomic studies
- cancer
- Classification
- Data analysis
- + 14
- R
- C
- CSS
circlize
Circular layout is an efficient way for the visualization of huge amounts of information. The circlize package provides an implementation of circular layout generation in R.
- Data analysis
- Data Science
- Data Visualization
- + 3
- R
CP2K
CP2K is a quantum chemistry and solid state physics software package running on graphics processing units and thousands of processing units. It is open-source and allows simulations, spectroscopy, vibrational analysis and energy minimization on a vast variety of theory levels.
- electronic structure
- GPU
- High performance computing
- + 5
- Fortran
- C
- Python
- + 13
COPASI
COPASI is an open source software for simulation and analysis of biochemical networks and their dynamics. It provides simulations using ODEs, SDEs, or Gillespie's stochastic simulation algorithm, with optional discrete events. COPASI provides several analyses, optimization, and parameter estimation.
- Dynamics
- optimization
- Parameter estimation
- + 3
- C++
- Java
- Fortran
- + 17
TOTEM_M
Code underlying: Topology Optimization of Thermo-Electro-Mechanical elements (TOTEM)
- Non-convexity
- Power constraint
- SIMP
- + 3
- Other
- Matlab
- HTML
- + 2
anvi'o
anvi'o is an open-source software platform for microbial 'omics research enabling analysis and visualization of 'omics data. In development since 2014, it is currently being maintained by the Ecosystem Data Science group at the Helmholtz Institute for Functional Marine Biodiversity.
- Data analysis
- Data Visualization
- Metagenomics
- + 4
- Python
- JavaScript
- HTML
- + 5
REMix
REMix is a powerful software for energy systems optimization. It can be used for the planning and techno-economical assessment of future multi-energy systems of any spatial, temporal and technological scope. REMix offers a wide range of methods and features that can be flexibly selected by the user.
- Energy
- Energy planning
- ESD
- + 5
- GAMS
- Python
- Dockerfile
Chemistry Development Kit
Open Source cheminformatics library.
- Cheminformatics
- Chemistry
- Computational Chemistry
- Java
- Pawn
- HTML
CORSIKA
A Monte Carlo framework for the simulation of particle showers initiated in the Earth's atmosphere (or dense media) by high-energy particles from the cosmos.
- Astroparticle Physics
- Matter
- Monte Carlo simulation
- Fortran
- C++
- C
- + 2