Predictor@home: Difference between revisions
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{{Infobox software | {{Infobox software | ||
| name = Predictor@home | | name = Predictor@home | ||
| logo = Predictor. | | logo = Predictor.gif | ||
| logo caption = Predictor@home project image | | logo caption = Predictor@home project image | ||
| screenshot = | | screenshot =Predictor.png | ||
| caption = | | caption = | ||
| description = Predictor@home was the first independent BOINC-based volunteer computing project, run by The Scripps Research Institute to predict protein tertiary structure from amino acid sequences, active from 2004 to 2009. | | description = Predictor@home was the first independent BOINC-based volunteer computing project, run by The Scripps Research Institute to predict protein tertiary structure from amino acid sequences, active from 2004 to 2009. | ||
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| sponsor = The Scripps Research Institute | | sponsor = The Scripps Research Institute | ||
| maintainer = Michela Taufer | | maintainer = Michela Taufer | ||
| released = {{Start date and age|2004| | | released = {{Start date and age|2004|05|04}} | ||
| completed = | | completed = | ||
| discontinued = {{Start date and age|2009|06|10}} | | discontinued = {{Start date and age|2009|06|10}} | ||
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| cpu performance = | | cpu performance = | ||
| website = {{URL| | | website = {{URL|http://predictor.chem.lsa.umich.edu/}} | ||
| license = | | license = | ||
}} | }} | ||
'''Predictor@home''' (also known as '''ProteinPredictorAtHome''' or '''P@H''') was a [[volunteer computing]] project that used the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) framework to predict [[protein structure prediction|protein tertiary structure]] from amino acid sequences. It was developed and run by [[Michela Taufer]] and [[Charles L. Brooks III]] at [[Scripps Research|The Scripps Research Institute]] in La Jolla, California.<ref name="taufer2005global">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems''. {{doi|10.1109/TPDS.2006.148}}</ref> The project holds the notable distinction of being the '''first independent BOINC-based project''' ever launched, going live on '''9 June 2004'''.<ref name="boinchistory">Marc Seil (17 January 2007). [https://isaac.ssl.berkeley.edu/forum_thread.php?id=1456 "BOINC History"]. BOINC message boards. Retrieved 2022-11-05.</ref><ref name="wikidata">{{cite web |url=https://www.wikidata.org/wiki/Q902260 |title=Predictor@home |publisher=Wikidata |access-date=2024-01-01}}</ref> | '''[https://web.archive.org/web/20081128162813/http://predictor.chem.lsa.umich.edu/ Predictor@home]''' (also known as '''ProteinPredictorAtHome''' or '''P@H''') was a [[volunteer computing]] project that used the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) framework to predict [[protein structure prediction|protein tertiary structure]] from amino acid sequences. It was developed and run by [[Michela Taufer]] and [[Charles L. Brooks III]] at [[Scripps Research|The Scripps Research Institute]] in La Jolla, California.<ref name="taufer2005global">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems''. {{doi|10.1109/TPDS.2006.148}}</ref> The project holds the notable distinction of being the '''first independent BOINC-based project''' ever launched, going live on '''9 June 2004'''.<ref name="boinchistory">Marc Seil (17 January 2007). [https://isaac.ssl.berkeley.edu/forum_thread.php?id=1456 "BOINC History"]. BOINC message boards. Retrieved 2022-11-05.</ref><ref name="wikidata">{{cite web |url=https://www.wikidata.org/wiki/Q902260 |title=Predictor@home |publisher=Wikidata |access-date=2024-01-01}}</ref> | ||
== Background == | == Background == | ||
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Predictor@home was deployed specifically to compete in CASP6 and to test whether volunteer computing could deliver meaningful improvements over traditional cluster computing for protein structure prediction. During this period, the project attracted '''6,786 users''' and accumulated over '''12 billion seconds''' of total compute time.<ref name="taufer2005global" /> | Predictor@home was deployed specifically to compete in CASP6 and to test whether volunteer computing could deliver meaningful improvements over traditional cluster computing for protein structure prediction. During this period, the project attracted '''6,786 users''' and accumulated over '''12 billion seconds''' of total compute time.<ref name="taufer2005global" /> | ||
The project significantly increased sampling capacity by '''one to two orders of magnitude''' compared to what was achievable with a local computer cluster, greatly improving the chances of finding near-native protein conformations. For 81% of the CASP6 target proteins, Predictor@home achieved more than 3,000 independent structure samples; for 48% of targets, it exceeded 10,000 samples.<ref name="taufer2005global" /> | The project significantly increased sampling capacity by '''one to two orders of magnitude''' compared to what was achievable with a local computer cluster, greatly improving the chances of finding near-native protein conformations. For 81% of the CASP6 target proteins, Predictor@home achieved more than 3,000 independent structure samples; for 48% of targets, it exceeded 10,000 samples.<ref name="taufer2005global" /> | ||
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During the peak of the CASP6 period, the server infrastructure could not keep pace with the rapid growth in participants, and user account creation was temporarily suspended to manage server load.<ref name="taufer2005pub" /> | During the peak of the CASP6 period, the server infrastructure could not keep pace with the rapid growth in participants, and user account creation was temporarily suspended to manage server load.<ref name="taufer2005pub" /> | ||
[[File:Scripps Florida Building B.JPG|thumb|340x340px|The Scripps Research Institute in La Jolla, California, where Predictor@home was developed.]] | |||
=== Later Development and Shutdown === | === Later Development and Shutdown === | ||
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The task assigned to each volunteer computer was to generate independent samples of protein conformations for a given target sequence and return the resulting structures to the central server. Because each work unit was independent, the sampling was [[embarrassingly parallel]], making volunteer computing an ideal fit. | The task assigned to each volunteer computer was to generate independent samples of protein conformations for a given target sequence and return the resulting structures to the central server. Because each work unit was independent, the sampling was [[embarrassingly parallel]], making volunteer computing an ideal fit. | ||
[[File:Predictor.png|thumb|340x340px|Predictor@home visualisation of a protein structure prediction run.]] | |||
=== Homogeneous Redundancy === | === Homogeneous Redundancy === | ||