Pinned Repositories
bamToFreq
Converts mapped next-generation sequencing reads in BAM format to the tabular frequency file format that is used by geno2pheno[ngs-freq]
bioconda-recipes
Conda recipes for the bioconda channel.
deeptime
Deep learning meets molecular dynamics.
gpcca
GPCCA: Generalized Perron Cluster Cluster Analysis program to coarse-grain reversible and non-reversible Markov State Models.
GROMACS-Crash-Course
2 days course to learn basic Linux terminal and GOMACS usage
msmtools
Tools for estimating and analyzing Markov state models
NestedCV
NestedCV: repeated nested stratified cross-validation
PlasmoFAB
pyGPCCA
pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state models.
use-remote-jupyter-notebook
How to use notebboks on your remote server in your local browser via ssh.
msmdev's Repositories
msmdev/pyGPCCA
pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state models.
msmdev/gpcca
GPCCA: Generalized Perron Cluster Cluster Analysis program to coarse-grain reversible and non-reversible Markov State Models.
msmdev/GROMACS-Crash-Course
2 days course to learn basic Linux terminal and GOMACS usage
msmdev/PlasmoFAB
msmdev/msmtools
Tools for estimating and analyzing Markov state models
msmdev/NestedCV
NestedCV: repeated nested stratified cross-validation
msmdev/use-remote-jupyter-notebook
How to use notebboks on your remote server in your local browser via ssh.
msmdev/bamToFreq
Converts mapped next-generation sequencing reads in BAM format to the tabular frequency file format that is used by geno2pheno[ngs-freq]
msmdev/bioconda-recipes
Conda recipes for the bioconda channel.
msmdev/deeptime
Deep learning meets molecular dynamics.
msmdev/geno2phenoTB
Machine learning based engine to predict Mycobacterium tuberculosis drug resistance using whole-genome sequencing data
msmdev/deeptime-vampnet-tensorflow-gpu-install
install the deeptime package vampnet (including nvidia drivers + tensorflow gpu install)
msmdev/fastqToFreq
Uses MinVar and bamToFreq to transform NGS reads (FASTQ) to frequency files (CSV)
msmdev/install-deeptime-time-lagged-autoencoder
Instructions to install the time-lagged autoencoder package from deeptime, based on pytorch.
msmdev/MalariaVaccineEfficacyPrediction
msmdev/post-aistats2017
New experiments
msmdev/print-on-nums11
how to move files to nums11 server and print them
msmdev/py-project-example
This repository is an example on how to structure you python project.
msmdev/python
msmdev/pytorch-gpu-install
Instructions for installing pytorch to run on GPU
msmdev/sampleproject
A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"
msmdev/sanoid
These are policy-driven snapshot management and replication tools which use OpenZFS for underlying next-gen storage. (Btrfs support plans are shelved unless and until btrfs becomes reliable.)
msmdev/shields
Concise, consistent, and legible badges in SVG and raster format
msmdev/smop
Small Matlab to Python compiler
msmdev/sra_read_downloader
A handy script for downloading reads from any kind of accession from the SRA.
msmdev/tbdb
Standard database for the TBProfiler tool
msmdev/TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
msmdev/tensorflow-build
TensorFlow binaries supporting AVX, FMA, SSE
msmdev/tensorflow-gpu-install-ubuntu-16.04
Tensorflow GPU install instructions for ubuntu 16.04 - Deep learning