python3-promod3

protein homology modelling engine - Python 3 package

ProMod3 is a modelling engine based on the OpenStructure computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms.

python3-escript

Escript/Finley finite elements Python3 system (with OpenMP)

Escript is a programming tool for implementing mathematical models in Python using the finite element method (FEM). Because users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis.

emacs-ocaml-merlin

editor service to develop in OCaml (emacs files)

This package provides an editor service for advanced integrated development environment (IDE) in the OCaml language both for the vim and emacs editors.

python3-biopython

Python3 library for bioinformatics

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

r-cran-bios2cor

GNU R from Biological Sequences and Simulations to Correlation

Analysis Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi: 10.1371/journal.pcbi.1006209>. An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) <doi: 10.1038/s41598-020-72766- 1>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).

r-cran-estimability

GNU R package providing tools for determining estimability of linear functions

The estimability package is a GNU R package providing tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly.