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BitTorrent, also referred to as simply torrent, is a communication protocol for peer-to-peer file sharing (P2P), which enables users to distribute data and electronic files over the Internet in a decentralized manner. The protocol is developed and maintained by Rainberry, Inc., and was first released in 2001.
BitComet is a cross-protocol BitTorrent, HTTP and FTP client written in C++ for Microsoft Windows and available in 52 different languages. Its first public release was version 0.28. The current BitComet logo has been used since version 0.50.
eXeem was a peer-to-peer (P2P) file sharing client using the BitTorrent protocol. eXeem was designed to replace the need for centralized trackers. It largely failed to achieve this goal, and the project was canceled and eXeem's network was shut down by the end of 2005.
BitTorrent is a proprietary adware BitTorrent client developed by Bram Cohen and Rainberry, Inc. used for uploading and downloading files via the BitTorrent protocol. BitTorrent was the first client written for the protocol. It is often nicknamed Mainline by developers denoting its official origins. Since version 6.0 the BitTorrent client has been a rebranded version of μTorrent. As a result, it is no longer open source. It is currently available for Microsoft Windows, Mac, Linux, iOS and Android. There are currently two versions of the software, "BitTorrent Classic" which inherits the historical version numbering, and "BitTorrent Web", which uses its own version numbering.
A BitTorrent tracker is a special type of server that assists in the communication between peers using the BitTorrent protocol.
Peer exchange or PEX is a communications protocol that augments the BitTorrent file sharing protocol. It allows a group of users that are collaborating to share a given file to do so more swiftly and efficiently.
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
Tribler is an open source decentralized BitTorrent client which allows anonymous peer-to-peer by default. Tribler is based on the BitTorrent protocol and uses an overlay network for content searching. Due to this overlay network, Tribler does not require an external website or indexing service to discover content. The user interface of Tribler is very basic and focused on ease of use instead of diversity of features. Tribler is available for Linux, Windows, and OS X.
GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. GenePattern is currently developed at the University of California, San Diego.
The following is a general comparison of BitTorrent clients, which are computer programs designed for peer-to-peer file sharing using the BitTorrent protocol.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
libtorrent is an open-source implementation of the BitTorrent protocol. It is written in and has its main library interface in C++. Its most notable features are support for Mainline DHT, IPv6, HTTP seeds and μTorrent's peer exchange. libtorrent uses Boost, specifically Boost.Asio to gain its platform independence. It is known to build on Windows and most Unix-like operating systems.
Integrated Genome Browser (IGB) is an open-source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
In the BitTorrent file distribution system, a torrent file or meta-info file is a computer file that contains metadata about files and folders to be distributed, and usually also a list of the network locations of trackers, which are computers that help participants in the system find each other and form efficient distribution groups called swarms. Torrent files are normally named with the extension .torrent.
The phenotype microarray approach is a technology for high-throughput phenotyping of cells. A phenotype microarray system enables one to monitor simultaneously the phenotypic reaction of cells to environmental challenges or exogenous compounds in a high-throughput manner. The phenotypic reactions are recorded as either end-point measurements or respiration kinetics similar to growth curves.
CloudBioLinux is an open-source project providing machine images for bioinformatics on cloud computing platforms. CloudBioLinux provides a build and deployment system which can deploy directly to desktop machines, to desktop Virtual Machines (VMs), or to cloud providers such as the Amazon Elastic Compute Cloud (EC2). The project also provides a pre-built Amazon Machine Image (AMI) for use on Amazon EC2, and downloadable pre-built virtual machine images for the desktop virtual machine software VirtualBox and for use on a private Eucalyptus cloud.
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g. different organism growth patterns or diseases). The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes, which are used for the analysis.
References
- ↑ https://github.com/preston/bittorious Source code
- ↑ http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0779-6 BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms
- ↑ Lee, Preston V.; Dinu, Valentin (January 1, 2014). "BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions". BMC Bioinformatics. 15 (1): 424. doi: 10.1186/s12859-014-0424-9 . PMC 4280033 . PMID 25528455.