Current release - Linux for Biotechnology V1

Features

• More than 1Gb of Biotechnology software and documentation, prebuilt for Linux
• All applications tested with Redhat (6.2) and SuSE (6.4) distributions
• New all RPM based installation, includes latest kpackage package manager
• Searchable integrated on-line documentation covering all included packages

If you know of any packages which we should include, please send us an email detailing the packages' functionality and the location of an ftp site where they can be found.
Ordering information : click here and then print the order form and send it to us with your payment, or download a postscript version.

Contents :

Volume 1 contains
• /opt/lfb/AE-2-0.i386.rpm - A sequence alignment editor
• /opt/lfb/Bastille-1.1.1.tar.gz - Linux security audit package
• /opt/lfb/DBI-1.14.tar.gz - DBI module for perl
• /opt/lfb/DEODAS-src-0.1-0.i386.rpm - DEgenerate Oligonucleotide Design & Analysis System
• /opt/lfb/Distutils-0.9.2.tar.gz - Distutils for old versions of python
• /opt/lfb/DomainFinder-1-0.i386.rpm - An interactive program for the determination and characterization of dynamical domains in proteins.
• /opt/lfb/EMBOSS-1.5-1.i386.rpm - EMB Open Source Software
• /opt/lfb/ESPript-1-9.i386.rpm - a program under development for loci in the forensic context.
• /opt/lfb/EdIt-1-0.i386.rpm - An automatic editor for DNA sequence data
• /opt/lfb/IBMJava2-JRE-1.3-1.1.i386.rpm - IBMJava2-1.3 JRE
• /opt/lfb/ImageJ-1-18.i386.rpm - Java image processing program inspired by NIH Image for the Macintosh
• /opt/lfb/JChemPaint-0-7.i386.rpm - JChemPaint is a Java 2 program for drawing 2D chemical structures
• /opt/lfb/MSPcrunch-2-0.i386.rpm - Postprocessor for blast-like applications
• /opt/lfb/MesaDemos-3.4.tar.gz - Demos for Mesa 3d-graphics libraries
• /opt/lfb/MesaLib-3.4.tar.gz - Mesa 3d-graphics libraries
• /opt/lfb/Msql-Mysql-modules-1.2215.tar.gz - MSQL add-on
• /opt/lfb/MyODBC-2.50.36-1.i386.rpm - MyODBC: an ODBC driver for MySQL
• /opt/lfb/MyODBC-2.50.36-1.src.rpm - MyODBC: an ODBC driver for MySQL
• /opt/lfb/MySQL-3.23.28-1.i386.rpm - MySQL: a very fast and reliable SQL database engine
• /opt/lfb/MySQL-bench-3.23.28-1.i386.rpm - MySQL - Benchmarks
• /opt/lfb/MySQL-client-3.23.28-1.i386.rpm - MySQL - Client
• /opt/lfb/MySQL-devel-3.23.28-1.i386.rpm - MySQL - Development header files and libraries
• /opt/lfb/MySQL-shared-3.23.28-1.i386.rpm - MySQL - Shared libraries
• /opt/lfb/NHGRI-Blastall-0-61.i386.rpm - Retrieve entries from sequence databases
• /opt/lfb/PSeq-Gen-1-1.i386.rpm - An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
• /opt/lfb/PVM-3-4.i386.rpm - Parallel Virtual Machine
• /opt/lfb/PackageContents.txt - Complete list of files in Biotech packages
• /opt/lfb/PyMOL-0-31.i386.rpm - molecular graphics program designed for rapid and efficient generation of high-quality molecular graphics animations.
• /opt/lfb/QDate-1-1.i386.rpm - Divergence estimator for sequences
• /opt/lfb/QuickPDB-1-0.i386.rpm - Protein databank browser
• /opt/lfb/README.TXT - Read this first
• /opt/lfb/RasMol-2-6.i386.rpm - Molecular visualization
• /opt/lfb/SPECS - Directory containing rpm generation data
• /opt/lfb/SampLin-1-4.i386.rpm - Data acquisition package
• /opt/lfb/Seq-Gen-1-1.i386.rpm - An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
• /opt/lfb/TipDate-1-1.i386.rpm - An application for the Monte Carlo simulation of protein equence evolution along phylogenetic trees
• /opt/lfb/abacus-0-63.i386.rpm - Analysis of Blake's Conjecture Using Simulations
• /opt/lfb/alfresco-0-92.i386.rpm - Comparitive sequence analysis
• /opt/lfb/allass-1-0.i386.rpm - ALLASS program for allelic association
• /opt/lfb/artemis-1-0.i386.rpm - DNA sequence viewer and annotation tool
• /opt/lfb/autorun - Autostart script for supermount users
• /opt/lfb/beta-1-0.i386.rpm - Estimation of alpha - Nonparametric linkage analysis
• /opt/lfb/bioperl-0.6-1.i386.rpm - Bioperl is an association of developers of public domain Perl tools for computational molecular biology.
• /opt/lfb/biopython-0-90.i386.rpm - biopython is an association of developers of public domain Python tools for computational molecular biology.
• /opt/lfb/bzip2-0.9.5d-2.i386.rpm - A file compression utility.
• /opt/lfb/ceph2map-1-0.i386.rpm - developed from crimap v2.4 for use with the map suite of programs.
• /opt/lfb/codonW-1-3.i386.rpm - CodonW is a package for codon usage analysis.
• /opt/lfb/deodas-0.1.2-1.i386.rpm - Degenerate Oligonuclotide Design & Analysis System interface
• /opt/lfb/dx-4.1-0.i386.rpm - Data Explorer
• /opt/lfb/dxsamples-4_0_tar.gz - Data samples for dx data visualization
• /opt/lfb/e-PCR-1-0.i386.rpm - Sequence mapping by Electronic PRC
• /opt/lfb/efetch-2-3.i386.rpm - Retrieve entries from sequence databases
• /opt/lfb/ensembl-0-6.i386.rpm - Automatically analyses and maintain the analysis on genomic DNA
• /opt/lfb/garlic-1-0.i386.rpm - Molecular visualization
• /opt/lfb/genie-1-0.i386.rpm - A Genetic simulator
• /opt/lfb/genpak-0-15.i386.rpm - DNA sequence manipulation
• /opt/lfb/gibbs-1-0.i386.rpm - Calculation of Probabilities and Likelihoods using gene identity indicators
• /opt/lfb/glib-1.2.8-ss-11.00.tar.gz - glib for use with GTK
• /opt/lfb/gmaes-1-0.i386.rpm - computes a gamma parameter that accounts rate variation among sites
• /opt/lfb/gnomemm-1.1.10-1.i386.rpm - A C++ interface for Gnome libs (a GUI library for X).
• /opt/lfb/gnomemm-devel-1.1.10-1.i386.rpm - Headers for developing programs that will use Gnome--.
• /opt/lfb/gtk+-1.2.8-ss-11.00.tar.gz - GTK add-on
• /opt/lfb/gtkGL-0.9-ss-10.20.tar.gz - GTK add-on
• /opt/lfb/gtkglarea-1.2.1.tar.gz - GTK add-on
• /opt/lfb/gtkglareamm-1.1.1.tar.gz - GTK add-on
• /opt/lfb/gtkmm-1.2.1-1.i386.rpm - A C++ interface for the GTK+ (a GUI library for X).
• /opt/lfb/gtkmm-devel-1.2.1-1.i386.rpm - Headers for developing programs that will use Gtk--.
• /opt/lfb/html - On-line documentation library for Biotechnology packages
• /opt/lfb/install - Directory of Installation guides in a variety of formats
• /opt/lfb/inventor-2.1.5-6.src.tar.gz - Open Inventor, an OpenGL toolkit
• /opt/lfb/jalview-1.7-5.i386.rpm - a java multiple alignment editor
• /opt/lfb/jmol-0.6-1.i386.rpm - an open-source molecule viewer and editor
• /opt/lfb/kmol-0.2-1.i386.rpm - Molecular weight calculator
• /opt/lfb/kpackage-1.3.10-3.i386.rpm - Kpackage is a graphical RPM package manager for KDE.
• /opt/lfb/ldb-2b-0.i386.rpm - Clonal mapping
• /opt/lfb/lesstif-0.88.1-1.i386.rpm - lesstif
• /opt/lfb/lfb-1-0.i386.rpm - Linux for Biotechnology baseline package
• /opt/lfb/libjpeg-6b-10.i386.rpm - A library for manipulating JPEG image format files.
• /opt/lfb/libjpeg-devel-6b-10.i386.rpm - Development tools for programs which will use the libjpeg library.
• /opt/lfb/libsigc++-1.0.1-1.i386.rpm - The Typesafe Signal Framework for C++
• /opt/lfb/libsigc++-devel-1.0.1-1.i386.rpm - development tools for the Typesafe Signal Framework for C++
• /opt/lfb/libtermcap-2.0.8-20.i386.rpm - A basic system library for accessing the termcap database.
• /opt/lfb/lintre-1-0.i386.rpm - Phylogenetic tests of the molecular clock and linearized tree
• /opt/lfb/melting-4-0.i386.rpm - nearest-neighbor computation of nucleic acid hybridization
• /opt/lfb/mira-1-4.i386.rpm - DNA shotgun sequence data assembly program
• /opt/lfb/mm.mysql.jdbc-1.2c.tar.gz - JDBC interface for MYSQL
• /opt/lfb/mmlib-1-0.i386.rpm - A C++ macromolecular class library.
• /opt/lfb/mmtool-1-0.i386.rpm - Molecular modelling tool
• /opt/lfb/moldy-2k-1.0.i386.rpm - a general-purpose molecular dynamics simulation program
• /opt/lfb/mysql++-1.7.8-1.i386.rpm - C++ interface to MySQL database
• /opt/lfb/mysql++-1.7.8-1.src.rpm - C++ interface to MySQL database
• /opt/lfb/mysqlgui-linux-static-1.7.2.tar.gz - GUI tools for MYSQL
• /opt/lfb/ncbi-6-1.i386.rpm - NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
• /opt/lfb/nessus-1.0.6-1.i386.rpm - Nessus security scanner
• /opt/lfb/nessus-client-1.0.6-1.i386.rpm - Nessus Gtk+ client.
• /opt/lfb/nessus-plugins-1.0.6-1.i386.rpm - Nessus plugins.
• /opt/lfb/njbtie-1-0.i386.rpm - Program for search all tie neighbor-joining trees and UPGMA trees and for bootstrapping
• /opt/lfb/ogl-sample.20000807.tgz - OpenGL test datasets
• /opt/lfb/oligomap-0-99.i386.rpm - OLIGOMAP is a tool to help researchers engineer restriction sites into oligonucleotides by silent mutagenesis
• /opt/lfb/openmotif-2.1.30-2_ICS.i386.rpm - The Open Motif runtime components.
• /opt/lfb/openmotif-devel-2.1.30-2_ICS.i386.rpm - The Open Motif development libraries and tools.
• /opt/lfb/orfind-1-0.i386.rpm - orfind is a command line version of ORF Finder
• /opt/lfb/pasu-1-0.i386.rpm - Probability and Statistics Utilities
• /opt/lfb/pdb2cif-2.3-3.i386.rpm - Convert PDB to CIF format
• /opt/lfb/pdbtool-2-0.i386.rpm - Molecular modelling tool
• /opt/lfb/performer.11212000.tar.gz - OpenGL tools
• /opt/lfb/pft-2-1.i386.rpm - a collection of experimental programs supporting the generalized profile format and search method of PROSITE and NUCSITE.
• /opt/lfb/pima-1-40.i386.rpm - Pattern-Induced Multi-sequence Alignment program
• /opt/lfb/plato-2-11.i386.rpm - Partial likelihoods expressed through optimisation
• /opt/lfb/popt-1.5-0.48.i386.rpm - A C library for parsing command line parameters.
• /opt/lfb/postgresql-7.0.3-2.i386.rpm - PostgreSQL client programs and libraries.
• /opt/lfb/postgresql-devel-7.0.3-2.i386.rpm - PostgreSQL development header files and libraries.
• /opt/lfb/postgresql-jdbc-7.0.3-2.i386.rpm - Files needed for Java programs to access a PostgreSQL database.
• /opt/lfb/postgresql-odbc-7.0.3-2.i386.rpm - The ODBC driver needed for accessing a PostgreSQL DB using ODBC.
• /opt/lfb/postgresql-perl-7.0.3-2.i386.rpm - Development module needed for Perl code to access a PostgreSQL DB.
• /opt/lfb/postgresql-python-7.0.3-2.i386.rpm - Development module for Python code to access a PostgreSQL DB.
• /opt/lfb/postgresql-server-7.0.3-2.i386.rpm - The programs needed to create and run a PostgreSQL server.
• /opt/lfb/postgresql-tcl-7.0.3-2.i386.rpm - A Tcl client library, and the PL/Tcl procedural language for PostgreSQL.
• /opt/lfb/postgresql-test-7.0.3-2.i386.rpm - The test suite distributed with PostgreSQL.
• /opt/lfb/postgresql-tk-7.0.3-2.i386.rpm - Tk shell and tk-based GUI for PostgreSQL.
• /opt/lfb/primer3-0-6.i386.rpm - Primer3 picks primers for PCR reactions,
• /opt/lfb/pseudoknots-1-0.i386.rpm - An extension of the Zuker MFOLD algorithm to optimal minimum energy prediction of pseudoknotted RNA structures
• /opt/lfb/pspp-0.3-0.i386.rpm - Statistical analysis package.
• /opt/lfb/puzzle-4.0-2.i386.rpm - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
• /opt/lfb/readline-2.2.1-5.i386.rpm - A library for reading and returning lines from a terminal.
• /opt/lfb/rhmapper-1-22.i386.rpm - A package for creating radiation hybrid maps
• /opt/lfb/rnabob-2-1.i386.rpm - Searches for RNA motifs in sequence databases
• /opt/lfb/sc_rate-1-2.i386.rpm - Evaluates the quality of any sequence alignment.
• /opt/lfb/seals-0-976.i386.rpm - System for Easy Analysis of Lots of Sequences
• /opt/lfb/sendbs-1-0.i386.rpm - Average nucleotide diversity within and between populations
• /opt/lfb/seqsplit-1-0.i386.rpm - Programs for running blastx on very long queries
• /opt/lfb/sgi-OpenInventor-clients-2.1.5-6.i386.rpm - Open Inventor Execution Only Environment
• /opt/lfb/sgi-OpenInventor-data-2.1.5-6.i386.rpm - Open Inventor Sample Data
• /opt/lfb/sgi-OpenInventor-devel-2.1.5-6.i386.rpm - Open Inventor 3D Development Toolkit
• /opt/lfb/sibs-2-0.i386.rpm - Sib Pair Analysis of Qualitative and Quantitative Traits
• /opt/lfb/simPCR-1-0.i386.rpm - check an sfind file from GCG for sequences that have homology to 2 opposite primers.
• /opt/lfb/sog-0-01.i386.rpm - algorithm to find the most parsimoneous nucleotide phylogenetic tree
• /opt/lfb/tRNAscan-SE-1-12.i386.rpm - a program for improved detection of transfer RNA genes in genomic sequence
• /opt/lfb/topal-2-01.i386.rpm - Package for Detecting Recombination Breakpoints
• /opt/lfb/treevolve-1-3.i386.rpm - a program to simulate the evolution of DNA sequences under different population dynamic scenarios
• /opt/lfb/usermode-1.20-1.i386.rpm - Graphical tools for certain user account management tasks.
• /opt/lfb/vanilla-1-0.i386.rpm - command line programs (written in Java) to provide simple access to the functionality available in PAL,
• /opt/lfb/vaspview-1-03.i386.rpm - scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package
• /opt/lfb/vnc-3.3.3r2_unixsrc.tgz - Virtual Network Computing source
• /opt/lfb/vnc-3.3.3r2_x86_linux_2.0.tgz - Virtual Network Computing linux binaries
• /opt/lfb/vnc-latest_doc.tgz - Virtual Network Computing documentation
• /opt/lfb/w2h-3-2.i386.rpm - WWW interface to the GCG Sequence Analysis Software Package
• /opt/lfb/webblast-2.0-8.i386.rpm - collection of Perl 5 programs which provide a simple data pipeline from Sequence machine to the web
• /opt/lfb/wise-2.1-22.i386.rpm - DNA and protein sequence comparisons

All packages must now be installed on a hard-disk prior to use. Installing the full set of LfB packages would occupy about 1.5 Gb.

Package installation is done using the 'kpackage' package managment program, or optionally any other RPM capable tool.

Some packages need to install system files and we recommend that you use the 'root' account for installation, and then chown the /opt/lfb directory tree to your regular user account afterwards.

The first step of the LfB installation is to choose where you wish to load the packages and then either

- mount a partition as /opt/lfb if you will be using the entire parititon for LfB

e.g.
mkdir /opt/lfb
mount /dev/hda3 /opt/lfb

- create a link /opt/lfb which points the base directory for your LfB packages. e.g

ln -s /mydisk1/tools/biotech /opt/lfb

Recommended installation procedure

• Prepare your disk for LfB packages (see above)
• Load the 'lfb-basic' package
• Browse the on-line documentation and decide which other packages to install
• Install other packages

Please refer to the installation manual for detailed instructions covering specific packages. This is available in a variety of formats in the 'install' directory on the cdrom, and can be downloaded in :

• Postscript format
• RTF format
• StarOffice format

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Although many packages CAN be manually unpacked and placed in any location (using rpm directives), we recommend that you use the provided kpackage program to ensure compatability with future releases of 'Linux for Biotechnology'.
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