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{{Infobox software
| logo = Simap logo.png
| screenshot = PRP align.jpg
| caption = A pairwise protein sequence alignment, the type of computation distributed by SIMAP work units
| description = SIMAP was a completed BOINC volunteer computing project that pre-calculated protein sequence similarities for a database used by bioinformaticians, developed at the Technical University of Munich, the Helmholtz Zentrum München and the University of Vienna.
| status = Completed
| category = Bioinformatics
| compute = CPU
| developer = Thomas Rattei
| author = Roland Arnold, Thomas Rattei, Hans-Werner Mewes
| sponsor = [[wikipedia:Technical University of Munich|Technical University of Munich]], [[wikipedia:Helmholtz Zentrum München|Helmholtz Zentrum München]], [[wikipedia:University of Vienna|University of Vienna]]
| maintainer = University of Vienna
| released = {{Start date and age|2004}}
| completed = No, the SIMAP database itself continued after leaving BOINC
| discontinued = {{Start date and age|2014|12|31}} (as a BOINC project)
| operating system = Windows, Linux, macOS, Android, other Unix-like systems

| stats as of = {{Start date and age|2013|02|17}}
| average performance = 24,168 GigaFLOPs
| active users = 5,378
| total users = 41,520
| active hosts = 11,654
| total hosts = 140,170
| rac =
| credit per day =
| gpu performance =
| cpu performance =
| website = {{URL|https://boincsimap.org/boincsimap/}}
}}

'''[https://web.archive.org/web/20130302044909/http://boincsimap.org/boincsimap/ SIMAP]''' ('''Similarity Matrix of Proteins''') was a [[wikipedia:BOINC|BOINC]]-based [[wikipedia:volunteer computing|volunteer computing]] project that maintained a large precalculated [[wikipedia:database|database]] of [[wikipedia:protein|protein]] sequence similarities for use in [[wikipedia:bioinformatics|bioinformatics]] research.<ref name="rattei2006">{{Cite journal
| last1 = Rattei | first1 = Thomas
| last2 = Arnold | first2 = Roland
| last3 = Tischler | first3 = Patrick
| last4 = Lindner | first4 = Daniel
| last5 = Stümpflen | first5 = Volker
| last6 = Mewes | first6 = Hans-Werner
| title = SIMAP: the similarity matrix of proteins
| journal = Nucleic Acids Research
| volume = 34
| issue = 90001
| pages = D252–D256
| year = 2006
| doi = 10.1093/nar/gkj106
| url = https://pmc.ncbi.nlm.nih.gov/articles/PMC1347468/
}}</ref><ref name="arnold2005">{{Cite journal
| last1 = Arnold | first1 = Roland
| last2 = Rattei | first2 = Thomas
| last3 = Tischler | first3 = Patrick
| last4 = Truong | first4 = Minh-Duc
| last5 = Stümpflen | first5 = Volker
| last6 = Mewes | first6 = Hans-Werner
| title = SIMAP--The similarity matrix of proteins
| journal = Bioinformatics
| volume = 21
| issue = Suppl 2
| pages = ii42–ii46
| year = 2005
| doi = 10.1093/bioinformatics/bti1107
| url = https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347468
}}</ref> The database was freely accessible for scientific purposes and aimed to cover essentially all publicly known protein sequences.<ref name="boincsimap-project">{{Cite web
| title = Similarity Matrix of Proteins - SIMAP
| url = https://boincsimap.org/boincsimap/project.php
| website = BOINCSIMAP
| access-date = 2026-07-04
}}</ref>

SIMAP was a joint project of the [[wikipedia:Technical University of Munich|Technical University of Munich]], the [[wikipedia:Helmholtz Zentrum München|Helmholtz Zentrum München]] and the [[wikipedia:University of Vienna|University of Vienna]].<ref name="wiki-simap">{{Cite web
| title = Similarity Matrix of Proteins
| url = https://en.wikipedia.org/wiki/Similarity_Matrix_of_Proteins
| website = [[wikipedia:Wikipedia|Wikipedia]]
| access-date = 2026-07-04
}}</ref> The project's BOINC-based computing arm, known as BOINCSIMAP, relied on volunteers donating idle [[wikipedia:CPU|CPU]] time to keep the similarity matrix up to date as new sequences were published.<ref name="boincsimap-project" />

== History ==
SIMAP was first described by Roland Arnold, Thomas Rattei and colleagues in 2005 as a database representing the protein similarity space, implemented with a calculation client capable of running both on Sun Gridengine clusters and as a BOINC application.<ref name="arnold2005" /> A more detailed description of the resulting database and its associated [[wikipedia:web service|web services]], including the ProtInfo query interface, was published the following year.<ref name="rattei2006" />

The project initially received new [[wikipedia:workunit|work units]] at the beginning of each month. From 2010 onward, the inclusion of environmental metagenomic sequences into the database required much longer periods of continuous computation, sometimes lasting several months, with updates typically occurring twice a year.<ref name="wiki-simap" /> In the fourth quarter of 2010, the project relocated from the Technical University of Munich to the University of Vienna after the failing electrical infrastructure at the Munich site made continued operation there impractical. Existing volunteers and users were required to detach from the old project URL and reattach to a new one at the University of Vienna.<ref name="wiki-simap" />

On 30 May 2014, project administrators announced that after a ten year history, SIMAP would leave the BOINC platform by the end of that year. The underlying SIMAP database and its research goals continued afterward using local hardware, described by the administrators as consisting of several hundred ordinary multi core [[wikipedia:CPU|CPUs]] running an [[wikipedia:Streaming SIMD Extensions|SSE]]-optimised version of the [[wikipedia:Smith-Waterman algorithm|Smith-Waterman algorithm]].<ref name="wiki-simap" />

== Methodology ==
SIMAP pre-calculated protein sequence similarities using the [[wikipedia:FASTA|FASTA]] search heuristic, restricted by a static raw score threshold and the BLOSUM50 substitution matrix, expressed as

<math>S \geq 80,\ \text{BLOSUM50}</math>

without limiting the maximum number of hits returned per sequence.<ref name="pmc-rattei2006">{{Cite web
| title = SIMAP: the similarity matrix of proteins
| url = https://pmc.ncbi.nlm.nih.gov/articles/PMC1347468/
| website = PubMed Central
| access-date = 2026-07-04
}}</ref> A separate application used [[wikipedia:hidden Markov model|hidden Markov models]] to search for [[wikipedia:protein domain|protein domains]] within the same set of sequences.<ref name="wiki-simap" />

Because SIMAP represented an all-against-all similarity space, the computational cost of keeping the matrix current grew with the square of the number of contained sequences,

<math>O(n^2)</math>

which is why the project relied on distributed volunteer computing rather than a single centralised system to keep pace with the growth of public sequence databases.<ref name="boincsimap-project" /> SIMAP took advantage of the approximate symmetry of alignment scores, treating the similarity of sequence A to sequence B as equal to that of B to A, which halved the amount of computation otherwise required and allowed the database to be updated incrementally as new sequences were added, without recomputing existing results.<ref name="pmc-rattei2006" />

[[File:Technische Universität München.jpg|thumb|The Technical University of Munich, where the SIMAP project began before relocating to the University of Vienna in 2010]]

== BOINC computing ==
On the BOINC platform, SIMAP work unit CPU times varied widely, ranging from about 15 minutes to 3 hours, with individual work units ranging from 1.5 to 2.2 [[wikipedia:megabyte|megabytes]] in size, averaging around 2 MB.<ref name="wiki-simap" /> Client software was provided that was optimised for [[wikipedia:Streaming SIMD Extensions|SSE]]-enabled processors and [[wikipedia:x86-64|x86-64]] architectures; non-SSE applications were also available for older processors, though these required additional manual installation steps.<ref name="wiki-simap" /> SIMAP supported [[wikipedia:Microsoft Windows|Windows]], [[wikipedia:Linux|Linux]], [[wikipedia:macOS|macOS]], [[wikipedia:Android (operating system)|Android]] and other Unix-like platforms.<ref name="wiki-simap" />

Because the database had, at various points, been brought up to date with all publicly known protein sequences and metagenomes, available work at any given time largely consisted of newly published sequences and metagenomes awaiting precomputation.<ref name="wiki-simap" />

[[File:Universität Wien, Hauptgebäude.jpg|thumb|The main building of the University of Vienna, which took over hosting of SIMAP from late 2010 until the project's departure from BOINC in 2014]]

== Applications ==
The SIMAP database was used by individual researchers investigating the evolution and function of specific proteins, as well as by other bioinformatics projects that accessed SIMAP data directly through its public interfaces and web services, including integration with the [[wikipedia:PEDANT|PEDANT]] genome annotation system.<ref name="boincsimap-project" /><ref name="pmc-rattei2006" /> Use of the database was offered free of charge for education and public research.<ref name="boincsimap-simap">{{Cite web
| title = SIMAP
| url = https://boincsimap.org/boincsimap/
| website = BOINCSIMAP
| access-date = 2026-07-04
}}</ref>

== Publications ==
The following papers, listed on the official [https://boinc.berkeley.edu/pubs.php#SIMAP BOINC publications page], report scientific results that made direct use of SIMAP's BOINC-computed data.

* {{Cite journal
| last1 = Arnold | first1 = Roland
| last2 = Goldenberg | first2 = Florian
| last3 = Mewes | first3 = Hans-Werner
| last4 = Rattei | first4 = Thomas
| title = SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
| journal = Nucleic Acids Research
| volume = 42
| issue = D1
| pages = D279–D284
| year = 2014
| doi = 10.1093/nar/gkt970
| url = https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt970
}}
* {{Cite conference
| last1 = Taylor | first1 = Simon J. E.
| last2 = Ghorbani | first2 = Mohammadmersad
| last3 = Mustafee | first3 = Navonil
| last4 = Turner | first4 = Stephen J.
| last5 = Kiss | first5 = Tamas
| last6 = Farkas | first6 = Daniel
| last7 = Kite | first7 = Shane
| last8 = Strassburger | first8 = Steffen
| title = Distributed computing and modeling & simulation: Speeding up simulations and creating large models
| conference = 2011 Winter Simulation Conference (WSC 2011)
| year = 2011
| doi = 10.1109/WSC.2011.6147748
| url = http://ieeexplore.ieee.org/document/6147748/
}}
* {{Cite journal
| last1 = Rattei | first1 = Thomas
| last2 = Tischler | first2 = Patrick
| last3 = Götz | first3 = Stefan
| last4 = Jehl | first4 = Marc-André
| last5 = Hoser | first5 = Jonathan
| last6 = Arnold | first6 = Roland
| last7 = Conesa | first7 = Ana
| last8 = Mewes | first8 = Hans-Werner
| title = SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
| journal = Nucleic Acids Research
| year = 2010
| doi = 10.1093/nar/gkp949
| url = https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp949
}}
* {{Cite journal
| last1 = Rattei | first1 = Thomas
| last2 = Tischler | first2 = Patrick
| last3 = Arnold | first3 = Roland
| display-authors = et al.
| title = SIMAP structuring the network of protein similarities
| journal = Nucleic Acids Research
| year = 2007
| doi = 10.1093/nar/gkm963
| url = https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm963
}}
* {{Cite journal
| last1 = Arnold | first1 = Roland
| last2 = Rattei | first2 = Thomas
| last3 = Tischler | first3 = Patrick
| last4 = Truong | first4 = Minh-Duc
| last5 = Stümpflen | first5 = Volker
| last6 = Mewes | first6 = Hans-Werner
| title = SIMAP--The similarity matrix of proteins
| journal = Bioinformatics
| volume = 21
| issue = Suppl 2
| pages = ii42–ii46
| year = 2005
| doi = 10.1093/bioinformatics/bti1107
| url = https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347468
}}

== See also ==
* [[BOINC Central]]
* [[World Community Grid]]

== External links ==
* {{URL|https://boincsimap.org/boincsimap/}}

== References ==
{{Reflist}}

[[Category:Completed BOINC projects]]
[[Category:Bioinformatics]]

SIMAP - Revision history

Al Piskun: first light