ArchBio Linux 15.1
A Bioinformatics / Cheminformatics LiveLinux distribution
Introduction
Already installed Software Packages
ArchBio LiveLinux comes with a lot of useful stuff already pre-installed, such as a TeXLive 2015 environment, Google Chromium webbrowser for access to online tools or web based data bases, several editors and development tools. This makes not only development of programs and pipelines convenient, but also usage of the tools and publication or presentation of results is made much easier. The desktop environment that comes with ArchBio Linux is Xfce4.
A list of Bioinformatics related ArchLinux packages that I maintain at the moment can be found here.
A list of pre-installed programs, libraries, and tools that are included in the ArchBio Linux distribution can be found below.
| Program name | Version | Description |
|---|---|---|
| barriers | 1.5.2 | Compute local minima and energy barriers of a landscape |
| bedtools | 2.24.0 | powerful toolset for genome arithmetic |
| bioperl-live-git | 20151119 | Perl modules for bioinformatics applications. |
| blast+-bin | 2.2.31 | New suite of BLAST tools that utilizes the NCBI C++ Toolkit |
| clustal-omega | 1.2.1 | Protein sequence alignment program |
| clustalw | 2.1 | Clustal W multiple sequence alignment program, version 2.0 |
| clustalx | 2.1 | Multiple alignment of nucleic acid and protein sequences |
| dialign | 2.2.1 | Multiple sequence alignment program |
| fragrep | 2 | Detect nucleotide pattern fragments in genomes that occur in a given order |
| gotohscan | 2.0_alpha | Search short sequences in large database sequences by computing all semi-global alignments |
| hmmer | 3.1b1 | Profile hidden Markov models (profile HMMs) for database searching using statistical descriptions of a sequence family's consensus |
| infernal | 1.1.1 | Search DNA sequence databases for RNA structure and sequence similarities using covariance models (CMs) |
| jalview | 2.8.2 | Bioinformatics Multiple Alignment Editor |
| kinwalker | 2.0 | Compute cotranscriptional folding trajectories of RNAs |
| locarna | 1.8.1 | Global and Local Alignment of RNAs |
| mafft | 7.245 | Multiple alignment program for amino acid or nucleotide sequences |
| meme | 4.10.2 | The MEME suite provides tools for discovering and using protein and DNA sequence motifs |
| muscle | 3.8.31 | multiple sequence comparison by log-expectation |
| phylip | 3.696 | A collection of programmes for evolutive genetics and inferring phylogenies |
| python-biopython | 1.65 | Freely available Python tools for computational molecular biology |
| readseq | 2.1.30 | A biosequence data format conversion tool |
| rnamicro | 1.1.4 | Distinguish miRNA precursor sequences from other (putative) non-coding RNAs |
| seaview | 4.5.4 | GUI for multiple sequence alignment and molecular phylogeny |
| snoreport | 1.3 | Computational identification of snoRNAs with unknown targets |
| tcoffee | 11.00.8cbe486 | An alignment tool for Protein, DNA and RNA sequences |
| treekin | 0.3.1 | Efficient computation of RNA folding dynamics |
| viennarna | 2.1.9 | RNA Secondary Structure Prediction and Comparison |
| Program name | Version | Description |
|---|---|---|
| chemtool | 1.6.14 | A small program for drawing chemical structures |
| openbabel | 2.3.2 | A library designed to interconvert between many file formats used in molecular modeling and computational chemistry |
| pymol | 1.7.6.0 | Molecular visualization system on an Open Source foundation |
| Program name | Version | Description |
|---|---|---|
| gnuplot | 5.0.1 | Plotting package which outputs to X11, PostScript, PNG, GIF, and others |
| grace | 5.1.25 | 2D plotting tool |
| gri | 2.12.23 | A script-based language for scientific graphics programming |
| lapack | 3.5.0 | Linear Algebra PACKage |
| blas | 3.5.0 | Linear Algebra PACKage |
| r | 3.2.1 | Language and environment for statistical computing and graphics |
| Program name | Version | Description |
|---|---|---|
| coreutils | 8.24 | The basic file, shell and text manipulation utilities of the GNU operating system |
| ddd | 3.3.12 | A graphical front-end for command-line debuggers such as GDB, JDB, pydb, perl debugger... |
| devtools | 20150606 | Tools for Arch Linux package maintainers |
| doxygen | 1.8.10 | |
| gdb | 7.10 | The GNU Debugger |
| ghex | 3.10.1 | A simple binary editor for the Gnome desktop |
| git | 2.5.3 | the fast distributed version control system |
| gitg | 3.17.1 | A GIT repository viewer based on GTK+ |
| graphviz | 2.38.0 | Graph visualization software |
| swig | 3.0.7 | Generate scripting interfaces to C/C++ code |
| valgrind | 3.10.1 | A tool to help find memory-management problems in programs |
| Program name | Version | Description |
|---|---|---|
| emacs | 24.5 | The extensible, customizable, self-documenting real-time display editor |
| gedit | 3.16.3 | A text editor for GNOME |
| meld | 3.14.0 | Visual diff and merge tool |
| nedit | 5.6a | A Unix text editor for programmers and general users |
| vim | 7.4.854 | |
| xournal | 0.4.8 | Notetaking and sketching application |
Download / Install
Get the latest ArchBio Live Linux: ArchBio-v15.1-x86_64.iso (architecture: x86 64bit, size: 1.9GB)
Prepare an USB-stick
Insert your USB-stick and make sure that it is not mounted.
Replace the
# dd bs=4M if=/path/to/iso/file of=/dev/sdX && sync
Alternatively, if you are using Windows, or MacOS X, you find out about more options how to prepare an USB stick for
the use of ArchBio in the corresponding ArchLinux Wiki Page
"USB flash installation media".