Biopuppy
Encyclopedia
BioPuppy is a minimal Linux
OS and electronic workbench. for bioinformatics
and computational biology
It has been designed to meet the needs of beginners, learners, students, staffs, and research scholars. BioPuppy is available as a live CD
, an installation CD or in USB Pen drive, and contains all the required software to boot the computer with ready to use bioinformatics tools. BioPuppy is based on Puppy Linux
. The other objective of BioPuppy is small in size and portability. The estimated size of BioPuppy is around 250MB.
BioPuppy Linux is derived from Puppy Linux. BioPuppy has all the features of Puppy Linux.
(full-featured) and Xvesa (lightweight). A wizard during the start-up process guides the user through setting up a graphical server appropriate for their video card and monitor. At the end of the wizard, the user will be presented with a desktop and window manager
; the default WM in most Puppy releases is JWM
. The 2.15 Community Edition provides the IceWM
manager by default.
comes with a specific package manager called PetGet. An older package manager, DotPup, was used in previous versions of the system and is still compatible.
BioPuppy also comes with a remaster tool that takes a snapshot of the current system and creates a remastered live-CD from it.
For more about package management see the Puppy package management article.
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
OS and electronic workbench. for bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
and computational biology
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
It has been designed to meet the needs of beginners, learners, students, staffs, and research scholars. BioPuppy is available as a live CD
Live CD
A live CD, live DVD, or live disc is a CD or DVD containing a bootable computer operating system. Live CDs are unique in that they have the ability to run a complete, modern operating system on a computer lacking mutable secondary storage, such as a hard disk drive...
, an installation CD or in USB Pen drive, and contains all the required software to boot the computer with ready to use bioinformatics tools. BioPuppy is based on Puppy Linux
Puppy Linux
Puppy Linux is a lightweight Linux distribution that focuses on ease of use. The entire system can be run from RAM, allowing the boot medium to be removed after the operating system has started...
. The other objective of BioPuppy is small in size and portability. The estimated size of BioPuppy is around 250MB.
BioPuppy Linux is derived from Puppy Linux. BioPuppy has all the features of Puppy Linux.
Features
- User friendly for those new to LinuxLinuxLinux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
. - Contains many necessary BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
tools (see the Biology tools included in BioPuppy). - Available in both Live CD/USB and Install option.
- BioPuppy will boot from a minimum PC/Laptop with 586 MHz CPU and 32Mb RAMRam-Animals:*Ram, an uncastrated male sheep*Ram cichlid, a species of freshwater fish endemic to Colombia and Venezuela-Military:*Battering ram*Ramming, a military tactic in which one vehicle runs into another...
. - Easy to install on hard drive, USB pen drive, or Compact Flash (CF) cards.
- Can save one's session while working as a Live CD/USB and restore it in the next boot.
- Very small in size (~200MB), but with many features.
- BioPuppy can run bioinformatics applications and programs and can store one's programs on the same CD-RW/Pen drive/Hard disk while one is working as a LiveCD.
- BioPuppy contains extensive help files for all its programs and bioinformatcis tools with screen shot.
- New versions can be easily updated.
- Bring all your programs, tools, movies, songs as well as your light weight BioPuppy Linux in a single USB Pen drive.
- BioPuppy Linux is a Free/Open SourceOpen sourceThe term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
software distribution for academic purpose - Includes all the features of Puppy LinuxPuppy LinuxPuppy Linux is a lightweight Linux distribution that focuses on ease of use. The entire system can be run from RAM, allowing the boot medium to be removed after the operating system has started...
Graphical User Interface (GUI)
BioPuppy comes with a choice of two graphical servers as like Puppy Linux: X.orgX.Org
X.Org refers to several things related to the X Window System:* X.Org, the organisation in charge of X standards from 1999 * The X.Org Foundation, a community-based foundation which took over X stewardship in 2004...
(full-featured) and Xvesa (lightweight). A wizard during the start-up process guides the user through setting up a graphical server appropriate for their video card and monitor. At the end of the wizard, the user will be presented with a desktop and window manager
Window manager
A window manager is system software that controls the placement and appearance of windows within a windowing system in a graphical user interface. Most window managers are designed to help provide a desktop environment...
; the default WM in most Puppy releases is JWM
JWM
JWM is a lightweight stacking window manager for the X Window System written by Joe Wingbermuehle. JWM is written in C and uses only Xlib at a minimum...
. The 2.15 Community Edition provides the IceWM
IceWM
IceWM is a stacking window manager for the X Window System graphical infrastructure, written by Marko Maček. It was coded from scratch in C++ and is released under the terms of the GNU Lesser General Public License...
manager by default.
Package management and distribution management
BioPuppy LinuxLinux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
comes with a specific package manager called PetGet. An older package manager, DotPup, was used in previous versions of the system and is still compatible.
BioPuppy also comes with a remaster tool that takes a snapshot of the current system and creates a remastered live-CD from it.
For more about package management see the Puppy package management article.
Biology tools added in BioPuppy Linux
- Sequence Analysis Tools
- Sim-4
- Tigr-Glimmer 2
- Genewise
- Muscle
- Sigma
- HMMERHMMERHMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences. It does this by comparing a profile-HMM to either a single sequence or a database of sequences...
- ClustalClustalClustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
X/W - mafft
- Artemis
- Structure Prediction Tools
- mfold
- gibbs
- FastLink
- Protein Structure Analysis Tools
- Phylogenetic Analysis tools
- Fast DNA
- Phylip
- Phylo_win
- Bioanalysis
- R-Project
- BioconductorBioconductorBioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology....
- Molecular Dynamics
- Protein Modeling
- ADUNAdunAdun may refer to:*a molecular dynamics simulation application*Adun , a fictional Protoss character in StarCraft*an alternative name for the ancient city of Dion, Palestine*another word for Dúnedain in J. R. R. Tolkien's legendarium...
- ADUN
- Docking
- MGL Tools
- Python Molecular Viewer (PMV)
- Vision
- System Biology
- Copasi-Complex Pathway Simulator from Virginia Bioinformatics InstituteVirginia Bioinformatics InstituteThe Virginia Bioinformatics Institute at Virginia Tech is a bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated...
- Copasi-Complex Pathway Simulator from Virginia Bioinformatics Institute
- On-line tools
- EMBOSSEMBOSSEMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
- BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
- Biobar
- Biofox
- EMBOSS