Chrome

• Run Chrome-Chromium in application mode

Chromium

• Run Chrome-Chromium in application mode

EM

• Write a numpy array to a mrc file using mrcfile
• Read a MRC file in python
• Extract a zone around a model from a MRC density file
• Automatic cropped (trimmed) of an EM density map in MRC format to get the minimal box size
• Resample MRC EM density map file using TEMPy
• Simulate a EM map from a pdb file using TEMPy

LaTeX

• Create pgf plot from python matplotlib
• Draw an helix with repeated protomers with LaTeX Tikz
• Semantic linefeeds in vim for easier git versioning of LaTeX documents
• bundledoc: bundle together all files needed to compile your LaTeX document
• Use latexdiff tool with git
• Mathjax in jekyll based blog
• LaTeX acronym package
• Figure size, font and LaTeX with matplotlib and python
• Truncate header in fancyhdr
• Use Jekyll with BibTeX
• LaTeX templates

LaTex

• Drawing stacked charts using tikz

NGL

• NGL viewer: multiple structure display and toggling representations
• NGL viewer: display residue in stick when clicking on it

ProxyCommand

• Use ProxyCommand with ssh to connect to host1 through host2

TapirGo

• Search in Jekyll blog site with TapirGo

autofs

• iPython 2.3.0-2 cannot save or autosave over mounted directory via sshfs
• Automount disk with sshfs when needed, with autofs

awk

• Filter stdout by printing file from a starting string using awk
• Simple slurm monitoring using awk
• Print the head and the tail of a file simultaneously with awk
• A simple script to renumber residue ids or atom serial number in PDB file using awk
• PDB selection with awk
• Merge multiple PDB files into one multimodels PDB file using awk
• Merge multiple PDB files into a unique multichain PDB file with awk
• Get the CA trace from a PDB file using awk
• Print alphabetical order with awk
• Split a multi chain pdb into one pdb file per chain using awk
• Fill missing values in a column formatted text file with awk
• Check if there is missing CA in a pdb file
• Convert 3-letters amino acid code to 1-letter code with awk
• Write data to B-factor column of a PDB file
• Split a multi model pdb from shell
• Awk: determine if a string is numeric
• Compute rmsd between two pdb with awk
• Sum over all columns with awk
• Run external command with awk
• Do not display long line with awk
• Work with protein data bank (pdb) files and awk
• awk if-else syntax

backup

• Efficient backuping system using Borgbackup

bash

• ZSH-Bash string manipulation
• Split a multi model pdb from shell
• Modulo in bash

bike

• A short history of traffic engineering

biopython

• Align two PDB files using Biopython

bluetooth

• Making a bluetooth speaker working with Debian 8.5

borg

• Efficient backuping system using Borgbackup

catdcd

• Process each frame of a DCD trajectory file using any script file using a standard PDB file as input
• Compute theoretical SAXS profile for each frame of a dcd format trajectory and the corresponding Chi value from experimental data

chimera

• Using chimera dockprep tool from command line
• Fix incomplete sidechains in a pdb file with a Chimera script
• Using chimera and javascript for browser based interactive view of macromolecular structure
• Recording movie with chimera

compression

• lzma compression in parallel

crashplan

• A quick Gnome 3 app indicator for crashplan
• Install Crashplan on a Raspberry Pi
• Get CrashPlan backup status using a shell command line on Linux

csplit

• Split a file based on new line pattern
• Split a multi model pdb from shell
• Work with protein data bank (pdb) files and awk

datamash

• Simple python clone of gnu datamash

dcd

• Select and save to DCD format from a molecular dynamics trajectory file using pymol from the shell command line
• Computing Solvent Accessible Surface Area (SASA) Calculation from a dcd trajectory file using MDTraj
• Process each frame of a DCD trajectory file using any script file using a standard PDB file as input

debian

• Fix the strange error message at boot after Debian update from Jessie to Stretch: 'error: no symbol table'
• Spell checking not working in LibreOffice
• Set exact time with ntp
• Check automatically for update in Debian
• Display the list of files installed along with a Debian Package

direnv

• git pull each time you enter a git repo directory using direnv

dssp

• Compute secondary structure content from a DCD trajectory file using python, MDAnalysis and DSSP

em

• Display basic information from a electron density map MRC file

etckeeper

• etckeeper - store etc directory in git, mercurial, bazaar, or darcs

ext4

• Tagging files using ext4 extended file attributes

fasta

• Extract a fasta sequence from a pdbfile using python

ffmpeg

• Using ffmpeg to create a movie from a list of image file

fish

• Set the default language (english) for the fish (shell)

ggplot

• Install ggplot for python in a virtualenv and use it with ipython notebook

git

• Git: save username and password for a git repo
• git pull each time you enter a git repo directory using direnv
• An automatic system to commit Git changes using Incron
• etckeeper - store etc directory in git, mercurial, bazaar, or darcs
• Create a Github gist and clone it transparently to a git repo
• Solve the git error: command not found: git-receive-pack
• Generate jekyll site locally and push source file and static web site to github
• Deploy jekyll site with git
• Use git to keep incremental backup of edited files
• Use latexdiff tool with git
• Git - tagging
• Git pull that run out of memory on the server

github

• Create a Github gist and clone it transparently to a git repo
• Generate jekyll site locally and push source file and static web site to github

gmail

• Configure ssmtp to use the mail Linux command line to send email with gmail

gnome

• Managing network interfaces using network manager CLI (nmcli)
• Random wallpaper from unsplash.com
• Reduce the size of the gnome-shell top bar
• A quick Gnome 3 app indicator for crashplan
• Manually add a file to the list of recently used files in Gnome
• Get notified when terminal commands end
• Set wallpaper to the National Geographic photo of the day for Gnome 3
• Randomly change desktop wallpaper on Gnome desktop

gnuplot

• Real time plot of the evolution of the number of files with gnuplot

gs

• Compress a PDF file using gs

html

• Generate an HTML slideshow using python

imagemagick

• How to rescale several images to same size
• Create animated gif from multiple images with ImageMagick

imp

• Compute theoretical SAXS profile for each frame of a dcd format trajectory and the corresponding Chi value from experimental data

incron

• An automatic system to commit Git changes using Incron

inkscape

• Make a pdf format slideshow from a unique svg file
• Interactive svg with inkscape
• Making a slideshow for a speech from Inkscape

ipython

• Running IPython from vim
• Run pymol interactively from IPython notebook
• Using pymol from ipython
• Local nbviewer: Simple read only viewer for ipython notebook files (ipynb)
• iPython 2.3.0-2 cannot save or autosave over mounted directory via sshfs

javascript

• Using chimera and javascript for browser based interactive view of macromolecular structure
• Generate an HTML slideshow using python

jekyll

• Search in Jekyll blog site with TapirGo
• Generate jekyll site locally and push source file and static web site to github
• Utility to create Jekyll blog template file from the command line interface
• zsh script to convert and format iPython notebook to jekyll markdown file
• Deploy jekyll site with git
• Paginate with jekyll
• Mathjax in jekyll based blog
• Use Jekyll with BibTeX

libreoffice

• Spell checking not working in LibreOffice

linux

• Managing network interfaces using network manager CLI (nmcli)
• Disable system bell
• Sequence alignment from the command line using mafft
• Random wallpaper from unsplash.com
• Reduce the size of the gnome-shell top bar
• Simple command to bookmark files
• Manually add a file to the list of recently used files in Gnome
• Simple script to monitor the memory usage of a process given its PID
• List and filter files based on timestamp
• Tagging files using ext4 extended file attributes
• Set the default language (english) for the fish (shell)
• Fix the strange error message at boot after Debian update from Jessie to Stretch: 'error: no symbol table'
• Get notified when terminal commands end
• Set wallpaper to the National Geographic photo of the day for Gnome 3
• Set exact time with ntp
• etckeeper - store etc directory in git, mercurial, bazaar, or darcs
• Create temp files and catch ctrl-C signal to cleanup
• Configure ssmtp to use the mail Linux command line to send email with gmail
• Linux redirection: read from and write to the same file. Use a sponge!
• Get CrashPlan backup status using a shell command line on Linux
• Check automatically for update in Debian
• Make a shell script exits if any subcommand failed
• Randomly change desktop wallpaper on Gnome desktop
• Display the list of files installed along with a Debian Package
• Adding vim data-source to Zeitgeist
• Setting higher screen resolution for external monitor on Linux
• Logical Volume Manager (LVM)
• Smart copy of photos from external memory card
• Formatting an external hard drive with parted
• Get a progress bar for a process in shell with pv -- Pipe Viewer --
• Split a multi model pdb from shell
• zsh tips and tricks
• Utility to create Jekyll blog template file from the command line interface
• Backup raspberry pi SD card
• Awk: determine if a string is numeric
• GNU parallel
• Restructured text syntax
• Renumber citations in restructured text
• Plotting from linux terminal
• Modulo in bash
• Automount disk with sshfs when needed, with autofs
• zsh script to convert and format iPython notebook to jekyll markdown file
• Deploy jekyll site with git
• Use git to keep incremental backup of edited files
• Real time plot of the evolution of the number of files with gnuplot
• Encode DVD into a mkv file with different subtitles and languages
• Syntax highlighting with pygments in the shell
• Configure Freedns (afraid.org) service with Inadyn

lvm

• Logical Volume Manager (LVM)

lzma

• lzma compression in parallel

mafft

• Sequence alignment from the command line using mafft

matplotlib

• Making better scatter plot: sort data points for scatter plots to plot first most frequent data
• Create pgf plot from python matplotlib
• matplotlib: scale colorbar to match graphic height
• Spring layout for annotating plot in matplotlib
• Plotting from linux terminal
• Figure size, font and LaTeX with matplotlib and python

mdanalysis

• Compute distance between two centers of mass from a DCD trajectory using MDAnalysis
• Compute pairwise RMSD between a given list of frame for a trajectory
• Compute the radius of gyration for each frame of a trajectory using MDAnalysis
• Compute secondary structure content from a DCD trajectory file using python, MDAnalysis and DSSP
• Compute timeseries RMSD from a dcd trajectory file using MDAnalysis
• Select a subset of atoms from a trajectory file with MDanalysis
• Extract a subset of frames from a DCD trajectory file with MDAnalysis
• Compute native contacts ratio from a dcd trajectory file with MD-Analysis
• Align dcd trajectory with MDAnalysis

mdtraj

• Computing Solvent Accessible Surface Area (SASA) Calculation from a dcd trajectory file using MDTraj

modeller

• Global distance test (GDT) and Longest Continuous Segments (LCS) with python
• Align two sequences using modeller and create a dictionnary mapping from the alignment object
• Structural alignment with modeller
• Repair a protein using Modeller and python
• Mutate a single residue in a pdb with python and Modeller
• Align pdb sequences using python and Modeller
• Modeller: generate an extended protein conformation from an initial PDB file
• Convert C alpha only protein structure to all atoms structure using Modeller

mpi

• mpi4py: some working examples
• mpi4py: Idle process occupies 100% CPU

mpi4py

• mpi4py: some working examples

mrc

• Write a numpy array to a mrc file using mrcfile
• Extract a zone around a model from a MRC density file
• Shift the origin of an EM map in MRC format using Tempy
• Automatic cropped (trimmed) of an EM density map in MRC format to get the minimal box size
• Resample MRC EM density map file using TEMPy
• Display basic information from a electron density map MRC file

mrcfile

• Print the header of a mrc file
• Read a MRC file in python

networkx

• Spring layout for annotating plot in matplotlib

nfs

• Configure NFS server and client

nmcli

• Managing network interfaces using network manager CLI (nmcli)

ntp

• Set exact time with ntp

numpy

• Quick method to get the index of every element of array y in array x

pandas

• Aggregate statistics from the Protein Data Bank

parallel

• Compute theoretical SAXS profile for each frame of a dcd format trajectory and the corresponding Chi value from experimental data
• `Argument list too long` error with GNU parallel
• Script to automatically build psf file from pdb in VMD
• GNU parallel

parted

• Formatting an external hard drive with parted

pdb

• Aggregate statistics from the Protein Data Bank
• Simple script to download a pdb file from the command line
• Using chimera dockprep tool from command line
• Fix incomplete sidechains in a pdb file with a Chimera script
• Simulate a EM map from a pdb file using TEMPy
• A simple script to renumber residue ids or atom serial number in PDB file using awk
• Simple alignment of two proteins using PCA
• Simple topological alignment of 2 proteins (which could be multichains) after prior structural alignment
• PDB selection with awk
• Merge multiple PDB files into one multimodels PDB file using awk
• Merge multiple PDB files into a unique multichain PDB file with awk
• Get the CA trace from a PDB file using awk
• Split a multi chain pdb into one pdb file per chain using awk
• Extract a fasta sequence from a pdbfile using python
• Extracting fields from a Protein Data Bank file (PDB) using python
• Check if there is missing CA in a pdb file
• Write data to B-factor column of a PDB file
• Split a multi model pdb from shell
• Script to automatically build psf file from pdb in VMD
• Compute rmsd between two pdb with awk
• Work with protein data bank (pdb) files and awk

pdf

• Compress a PDF file using gs

photo

• Set wallpaper to the National Geographic photo of the day for Gnome 3

photos

• Smart copy of photos from external memory card

pulseaudio

• Making a bluetooth speaker working with Debian 8.5

pv

• Transfer file through ssh using tar and pv
• Get a progress bar for a process in shell with pv -- Pipe Viewer --

pymol

• Get the topology and coordinates from a PDB file using pymol
• Merge 2 pdbs using pymol from the shell CLI
• Select and save to DCD format from a molecular dynamics trajectory file using pymol from the shell command line
• Using pymol alter command from command line
• Use pymol command iterate from the shell command line
• Extract sequence from a PDB file from the command line using pymol
• Select atoms in a PDB file from the terminal command line using pymol
• Compute the global distance test (GDT) with pymol
• Run pymol interactively from IPython notebook
• Using pymol from ipython

pypdb

• Aggregate statistics from the Protein Data Bank

python

• PCA on dual space
• Print the header of a mrc file
• Get the topology and coordinates from a PDB file using pymol
• Write a numpy array to a mrc file using mrcfile
• Read a MRC file in python
• Extract a zone around a model from a MRC density file
• Installing tensorflow with conda
• Using pymol alter command from command line
• Use pymol command iterate from the shell command line
• Extract sequence from a PDB file from the command line using pymol
• Select atoms in a PDB file from the terminal command line using pymol
• Aggregate statistics from the Protein Data Bank
• Running IPython from vim
• Quick method to get the index of every element of array y in array x
• Python: Insert element in a list and keep it sorted
• Compute the global distance test (GDT) with pymol
• Shift the origin of an EM map in MRC format using Tempy
• Automatic cropped (trimmed) of an EM density map in MRC format to get the minimal box size
• Display basic information from a electron density map MRC file
• Computing Solvent Accessible Surface Area (SASA) Calculation from a dcd trajectory file using MDTraj
• Using chimera dockprep tool from command line
• Fix incomplete sidechains in a pdb file with a Chimera script
• Simulate a EM map from a pdb file using TEMPy
• Simple python clone of gnu datamash
• Align two PDB files using Biopython
• Global distance test (GDT) and Longest Continuous Segments (LCS) with python
• Align two sequences using modeller and create a dictionnary mapping from the alignment object
• Simple alignment of two proteins using PCA
• Install ggplot for python in a virtualenv and use it with ipython notebook
• Simple topological alignment of 2 proteins (which could be multichains) after prior structural alignment
• Installing Borg(backup) using pip and virtualenv (no root install)
• Run pymol interactively from IPython notebook
• Generate an HTML slideshow using python
• Using pymol from ipython
• Extract a fasta sequence from a pdbfile using python
• Structural alignment with modeller
• Skew normal distribution in python
• mpi4py: some working examples
• Compute distance between two centers of mass from a DCD trajectory using MDAnalysis
• Stream data in real time with python
• Compute the radius of gyration for each frame of a trajectory using MDAnalysis
• Repair a protein using Modeller and python
• Mutate a single residue in a pdb with python and Modeller
• Align pdb sequences using python and Modeller
• Compute the shortest path on a grid using python
• Compute secondary structure content from a DCD trajectory file using python, MDAnalysis and DSSP
• mpi4py: Idle process occupies 100% CPU
• Extracting fields from a Protein Data Bank file (PDB) using python
• Modeller: generate an extended protein conformation from an initial PDB file
• Temporarily suppress console output in python (From: Dave Smith's Blog)
• Making better scatter plot: sort data points for scatter plots to plot first most frequent data
• Compute timeseries RMSD from a dcd trajectory file using MDAnalysis
• Convert C alpha only protein structure to all atoms structure using Modeller
• Moving average in python
• Create pgf plot from python matplotlib
• matplotlib: scale colorbar to match graphic height
• iPython 2.3.0-2 cannot save or autosave over mounted directory via sshfs
• Progress reporting in python
• Select a subset of atoms from a trajectory file with MDanalysis
• Extract a subset of frames from a DCD trajectory file with MDAnalysis
• Compute native contacts ratio from a dcd trajectory file with MD-Analysis
• Align dcd trajectory with MDAnalysis
• Spring layout for annotating plot in matplotlib
• Plotting from linux terminal
• Reload library automatically in IPython notebook
• Computing RMSD efficiently with pyRMSD in python
• Geodesic distance transform in python
• zsh script to convert and format iPython notebook to jekyll markdown file
• Metadynamics on a 2D surface potential with python
• Adaptive sampling of a 2D surface potential by Markov Chain Monte Carlo with python
• Simple Markov chain Monte Carlo (MCMC) algorithm in python
• Sum elements of an array from given labels, in python, without for loop
• Elastic network model of proteins with python
• n-curve Gaussian fitting with Gaussian mixture models
• Smoothed data histogram with SOM
• WHAM: The Weighted Histogram Analysis Method
• Transition networks with python
• Figure size, font and LaTeX with matplotlib and python

qrcode

• Encode a string into a qrcode en display it using qrencode

qrencode

• Encode a string into a qrcode en display it using qrencode

raspberry-pi

• Install Crashplan on a Raspberry Pi
• Backup raspberry pi SD card
• Git pull that run out of memory on the server

restructured-text

• Restructured text syntax
• Renumber citations in restructured text

saxs

• Compute theoretical SAXS profile for each frame of a dcd format trajectory and the corresponding Chi value from experimental data

science

• Sequence alignment from the command line using mafft
• Simulate a EM map from a pdb file using TEMPy
• Process each frame of a DCD trajectory file using any script file using a standard PDB file as input
• Global distance test (GDT) and Longest Continuous Segments (LCS) with python
• Simple topological alignment of 2 proteins (which could be multichains) after prior structural alignment
• Using chimera and javascript for browser based interactive view of macromolecular structure
• Extract a fasta sequence from a pdbfile using python
• Download electron microscopy density map from the EMDataBank directly from shell
• Skew normal distribution in python
• Repair a protein using Modeller and python
• Mutate a single residue in a pdb with python and Modeller
• Align pdb sequences using python and Modeller
• Compute the shortest path on a grid using python
• Modeller: generate an extended protein conformation from an initial PDB file
• Convert C alpha only protein structure to all atoms structure using Modeller
• Slideshow: Unraveling protein functional motions using Self-Organizing Maps.
• Compute native contacts ratio from a dcd trajectory file with MD-Analysis
• Compute theoretical SAXS profile for each frame of a dcd format trajectory and the corresponding Chi value from experimental data
• Align dcd trajectory with MDAnalysis
• Computing RMSD efficiently with pyRMSD in python
• New publication: An automatic tool to analyze and cluster macromolecular conformations based on Self-Organizing Maps
• Metadynamics on a 2D surface potential with python
• Adaptive sampling of a 2D surface potential by Markov Chain Monte Carlo with python
• Simple Markov chain Monte Carlo (MCMC) algorithm in python
• Elastic network model of proteins with python
• Smoothed data histogram with SOM
• WHAM: The Weighted Histogram Analysis Method
• Transition networks with python

scikit-learn

• n-curve Gaussian fitting with Gaussian mixture models

shell

• Simple script to monitor the memory usage of a process given its PID
• List and filter files based on timestamp
• Download electron microscopy density map from the EMDataBank directly from shell
• Create temp files and catch ctrl-C signal to cleanup
• Linux redirection: read from and write to the same file. Use a sponge!
• Smart copy of photos from external memory card
• Get a progress bar for a process in shell with pv -- Pipe Viewer --
• Split a multi model pdb from shell
• Modulo in bash

slideshow

• Slideshow: Unraveling protein functional motions using Self-Organizing Maps.

slurm

• Simple slurm monitoring using awk

squashfs

• Simple script to mount or unmount a squashfs archive
• Simple script to automate the creation of squashfs archives
• Creating and using squashed file systems

ssh

• Transfer file through ssh using tar and pv
• Automatic reconnection with sshfs
• Automatically change the tmux pane color for SSH session
• Use ProxyCommand with ssh to connect to host1 through host2

sshfs

• Automatic reconnection with sshfs
• iPython 2.3.0-2 cannot save or autosave over mounted directory via sshfs
• Automount disk with sshfs when needed, with autofs

ssmtp

• Configure ssmtp to use the mail Linux command line to send email with gmail

svg

• Make a pdf format slideshow from a unique svg file
• Interactive svg with inkscape
• Making a slideshow for a speech from Inkscape

tag

• Tagging files using ext4 extended file attributes

tar

• Transfer file through ssh using tar and pv

tempy

• Shift the origin of an EM map in MRC format using Tempy
• Automatic cropped (trimmed) of an EM density map in MRC format to get the minimal box size
• Resample MRC EM density map file using TEMPy
• Display basic information from a electron density map MRC file
• Simulate a EM map from a pdb file using TEMPy

tensorflow

• Installing tensorflow with conda

tikz

• Drawing stacked charts using tikz
• Draw an helix with repeated protomers with LaTeX Tikz

tmux

• Automatically change the tmux pane color for SSH session

unsplash

• Random wallpaper from unsplash.com

vim

• Adding vim data-source to Zeitgeist
• Coding style: highlight text that goes over the 80 column limit in vim
• Vim scrolling option
• Semantic linefeeds in vim for easier git versioning of LaTeX documents
• Vim: find exactly n starting spaces
• Word wrap without line breaks with vim
• Spell check in vim

virtualenv

• Install ggplot for python in a virtualenv and use it with ipython notebook
• Installing Borg(backup) using pip and virtualenv (no root install)

vmd

• Script to automatically build psf file from pdb in VMD

zeitgeist

• Adding vim data-source to Zeitgeist

zsh

• How to rescale several images to same size
• Simple command to bookmark files
• ZSH-Bash string manipulation
• List and filter files based on timestamp
• zsh: show right prompt with date ONLY when command is executed
• ZSH string manipulation: split string
• Simple zsh calculator
• Smart copy of photos from external memory card
• Split a multi model pdb from shell
• Get a range of script arguments in zsh
• Work with arrays in zsh
• Increment value in zsh
• Script to automatically build psf file from pdb in VMD
• zsh tips and tricks
• Utility to create Jekyll blog template file from the command line interface
• zsh script to convert and format iPython notebook to jekyll markdown file