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.