Similarity Matrix of Proteins (SIMAP) is a

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spa ...

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

similarities created using

volunteer computing Volunteer computing is a type of distributed computing in which people donate their computers' unused resources to a research-oriented project, and sometimes in exchange for credit points. The fundamental idea behind it is that a modern desktop co ...

. It is freely accessible for scientific purposes. SIMAP uses the

FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

algorithm to precalculate protein similarity, while another application uses

hidden Markov model A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an ob ...

s to search for

protein domain In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist o ...

s. SIMAP is a joint project of the

Technical University of Munich The Technical University of Munich (TUM or TU Munich; german: Technische Universität München) is a public research university in Munich, Germany. It specializes in engineering, technology, medicine, and applied and natural sciences. Establis ...

, the

Helmholtz Zentrum München Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), also known as Helmholtz Munich, is a member of the Helmholtz Association of German Research Centres. It was founded in 1960 and is a joint venture by the Fed ...

, and the

University of Vienna The University of Vienna (german: Universität Wien) is a public research university located in Vienna, Austria. It was founded by Duke Rudolph IV in 1365 and is the oldest university in the German-speaking world. With its long and rich h ...

Project

The project usually got new work units at the beginning of each month. More recently, (2010), inclusion of environmental sequences into the database has required longer periods of activity, several months of continuous work for example. Typically, these updates occurred twice each year. In the fourth quarter of 2010, the project relocated to the

due to the failing electrical infrastructure at the Technical University of Munich. Part of this exercise involved the creation of a project specific

URL A Uniform Resource Locator (URL), colloquially termed as a web address, is a reference to a web resource that specifies its location on a computer network and a mechanism for retrieving it. A URL is a specific type of Uniform Resource Identifi ...

requiring existing volunteers and users to detach/reattach to the project. On May 30, 2014, it was announced by project administrators that after a 10-year history, SIMAP would be leaving

BOINC The Berkeley Open Infrastructure for Network Computing (BOINC, pronounced – rhymes with "oink") is an open-source middleware system for volunteer computing (a type of distributed computing). Developed originally to support SETI@home, it becam ...

by the end of 2014. SIMAP research, however, will go forward with the use of local hardware consisting of "ordinary multi-core CPUs (some hundreds), crunching a SSE-optimized version of the Smith-Waterman algorithm."

Computing platform

SIMAP used the

Berkeley Open Infrastructure for Network Computing The Berkeley Open Infrastructure for Network Computing (BOINC, pronounced – rhymes with "oink") is an open-source middleware system for volunteer computing (a type of distributed computing). Developed originally to support SETI@home, it beca ...

(BOINC)

distributed computing A distributed system is a system whose components are located on different networked computers, which communicate and coordinate their actions by passing messages to one another from any system. Distributed computing is a field of computer sci ...

platform.

Application performance notes

Work unit CPU times varied widely, ranging between 15 minutes and 3 hours. Work units varied in size from 1.5 to 2.2 MB each, averaging around 2 MB. SIMAP provided client software optimized for SSE enabled processors and

x86-64 x86-64 (also known as x64, x86_64, AMD64, and Intel 64) is a 64-bit version of the x86 instruction set, first released in 1999. It introduced two new modes of operation, 64-bit mode and compatibility mode, along with a new 4-level paging ...

processors. For older processors non SSE applications are provided but require manual installation steps to be taken.

Operating Systems An operating system (OS) is system software that manages computer hardware, software resources, and provides common daemon (computing), services for computer programs. Time-sharing operating systems scheduler (computing), schedule tasks for ef ...

supported by SIMAP are

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which i ...

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ...

Mac OS Two major famlies of Mac operating systems were developed by Apple Inc. In 1984, Apple debuted the operating system that is now known as the "Classic" Mac OS with its release of the original Macintosh System Software. The system, rebranded " ...

, Android, and other UNIX platforms. Since the database had sometimes been completed with all publicly known

protein sequence Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesi ...

s and

metagenome Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or micro ...

s having been precalculated by the project, the work available consisted of newly published protein sequences and metagenomes that needed to be precomputed for SIMAP.

References

External links

* {{DEFAULTSORT:Similarity Matrix of Proteins Science in society Free science software Volunteer computing projects

Project

Computing platform

Application performance notes

See also

References

External links