The ProteomeCommons.org Tranche Network is a secure peer-to-peer (P2P) network of computers used to share scientific data, primarily proteomics data. Tranche is sometimes referred to as "a BitTorrent for scientific" data because it works similar to the popular BitTorrent tool; however, Tranche includes many security features that make it more appropriate for sharing scientific data sets. The Tranche tools are free to use, open-source, and may be found at http://tranche.proteomecommons.org.
History of Tranche
The ProteomeCommons.org Tranche project started as part of Jayson Falkner's PhD work at the University of Michigan, Ann Arbor, in 2005. The work was done as part of the National Resource for Proteomics and Pathways (Grant# P41 RR018627), directed by Philip C. Andrews. Early versions of Tranche were used to aid in the collection of data for the ABRF sPRG 2006 study, and the first version of the Tranche project was presented at the 2006 ASMS in Seattle, WA. Jayson Falkner graduated in 2008 and work on Tranche is continued by the Tranche group at the University of Michigan and by Single Organism Software Inc (SOSI), a company co-founded by Jayson.
Tranche quickly became a widely used solution to the data sharing problem in proteomics. Several proteomics journals have made recommendations that require data sharing; however, none of those recommendations actually proposed a method of sharing the data. Tranche provides an ideal, free-to-use solution, which is supported a recommendation for use in Nature Biotechnology editor's note. Tranches growth and use can further be observed by the statistics collected and displayed on the tranche.proteomecommons.org web page. Currently more than 5,000 data sets are on-line, including several million files and multiple terabytes of data.
Tranche has been used by several other proteomics resources, including the obvious use by the ProteomeCommons.org data pages. The ProteinPedia project is another example use that annotates proteomics information and links to raw data stored in Tranche. The University of Vanderbilt's Medical Center also uses Tranche to archive several data sets related to its bioinformatics tools, primarily work done by David Tabb. A more verbose list of similar collaborations can be found at http://tranche.proteomecommons.org/examples. While use of Tranche may be completely hidden from users, several groups rely on the Tranche website to directly provide homepages for archives of data that has been collected. The National Cancer Institute (NCI) Mouse Models and CPTAC initatives are two examples of such work, but both the ABRF and HUPO organizations use Tranche in a similar fashion.
Use of Tranche has spread from proteomics in to other disciplines of science, including glycomics, metabalomics, and 2D gel data. However, the ProteomeCommons.org Tranche Network still primarily consists of tandem mass spectrometry proteomics data. Development and support of the Tranche codebase and tools continues to be provided by the University of Michigan. Commercial services related to storing data in Tranche and developing code for Tranche can be obtained from SOSI. The entire Tranche project is open-source, free to use, and anyone may participate in development of the code base.
Key Features of Tranche
Technical presentations and posters are archived on the Tranche download page; however, the key features of Tranche are summarized below.
* Multiple computers distribute the task of hosting data
** Data is typically compressed () and encrypted ()
** Data is split in to 1MB chunks for efficient distribution
* All data is digitally signed by the user(s) that uploaded it
** Files can be blocked if they are uploaded by untrusted users
** Files can be revoked/delete from the network if desired
** Downloads can be verified to ensure the content is as expected, e.g. not a virus
* All data is identified by a digital hash named the "Tranche Hash"
** MD5 + SHA-1 + SHA-256 + file length comprise a "Tranche Hash"
** Uploading the same file twice doesn't require more disk space
** No . Data can be looked up regardless of what server it is currently on
** The hashes enable an efficient, index free method of looking up data on a Tranche network
** Post download, the Tranche hash can be used to check that a file's contents haven't changed since publication
* Clear licensing terms when data is uploaded, including beta-support for
How is Tranche Different than BitTorrent
While Tranche is a P2P tool similar to BitTorrent significant changes were made so that Tranche would be appropriate for the sharing of scientific data sets, or in a broader sense, any data that requires tracking of information related to what users originally uploaded the data. Here is a short list of how Tranche is similar and different to BitTorrent.
Similarities compared to BitTorrent
*Uses P2P practices to efficient share data and scale well with large volumes of users
*Free to use and open-source
Differences compared to BitTorrent
*Licensing terms for use of data must be selected prior to upload
*Users are not anonymous. All data have signatures from the uploading users.
*Data may be revoked from the network if needed
*Individual files may be downloaded from an upload that includes multiple files, e.g. need not download the entire ZIP in order to get one file.
*Data may be passphrase protected (AES 256 encryption) for restricted access
*Primarily used for sharing scientific data. No known illicit content on the network.
Related Publications
*Archive of Tranche Presentations and Posters
*Andrews PC and Falkner JA, "Open Access to Proteomics Data: A Valuable Resource for Biology and Medicine", Journal of Proteome Research 6(6): pp 2047-2048, 2007
*Falkner JA, Hill JA, Andrews PC, "Proteomics FASTA Archive and Reference Resource", Proteomics (2008)
*Falkner JA, Andrews PC, "Publicly dissemination large amounts of proteomics data in a secure and scalable fashion", http://tranche.proteomecommons.org (in submission)
*Falkner JA, Ulintz PJ, and Andrews PC, "A Code and Data Archival and Dissemination Tool for the Proteomics Community", American Biotechnology Laboratory, Apr, 2006
History of Tranche
The ProteomeCommons.org Tranche project started as part of Jayson Falkner's PhD work at the University of Michigan, Ann Arbor, in 2005. The work was done as part of the National Resource for Proteomics and Pathways (Grant# P41 RR018627), directed by Philip C. Andrews. Early versions of Tranche were used to aid in the collection of data for the ABRF sPRG 2006 study, and the first version of the Tranche project was presented at the 2006 ASMS in Seattle, WA. Jayson Falkner graduated in 2008 and work on Tranche is continued by the Tranche group at the University of Michigan and by Single Organism Software Inc (SOSI), a company co-founded by Jayson.
Tranche quickly became a widely used solution to the data sharing problem in proteomics. Several proteomics journals have made recommendations that require data sharing; however, none of those recommendations actually proposed a method of sharing the data. Tranche provides an ideal, free-to-use solution, which is supported a recommendation for use in Nature Biotechnology editor's note. Tranches growth and use can further be observed by the statistics collected and displayed on the tranche.proteomecommons.org web page. Currently more than 5,000 data sets are on-line, including several million files and multiple terabytes of data.
Tranche has been used by several other proteomics resources, including the obvious use by the ProteomeCommons.org data pages. The ProteinPedia project is another example use that annotates proteomics information and links to raw data stored in Tranche. The University of Vanderbilt's Medical Center also uses Tranche to archive several data sets related to its bioinformatics tools, primarily work done by David Tabb. A more verbose list of similar collaborations can be found at http://tranche.proteomecommons.org/examples. While use of Tranche may be completely hidden from users, several groups rely on the Tranche website to directly provide homepages for archives of data that has been collected. The National Cancer Institute (NCI) Mouse Models and CPTAC initatives are two examples of such work, but both the ABRF and HUPO organizations use Tranche in a similar fashion.
Use of Tranche has spread from proteomics in to other disciplines of science, including glycomics, metabalomics, and 2D gel data. However, the ProteomeCommons.org Tranche Network still primarily consists of tandem mass spectrometry proteomics data. Development and support of the Tranche codebase and tools continues to be provided by the University of Michigan. Commercial services related to storing data in Tranche and developing code for Tranche can be obtained from SOSI. The entire Tranche project is open-source, free to use, and anyone may participate in development of the code base.
Key Features of Tranche
Technical presentations and posters are archived on the Tranche download page; however, the key features of Tranche are summarized below.
* Multiple computers distribute the task of hosting data
** Data is typically compressed () and encrypted ()
** Data is split in to 1MB chunks for efficient distribution
* All data is digitally signed by the user(s) that uploaded it
** Files can be blocked if they are uploaded by untrusted users
** Files can be revoked/delete from the network if desired
** Downloads can be verified to ensure the content is as expected, e.g. not a virus
* All data is identified by a digital hash named the "Tranche Hash"
** MD5 + SHA-1 + SHA-256 + file length comprise a "Tranche Hash"
** Uploading the same file twice doesn't require more disk space
** No . Data can be looked up regardless of what server it is currently on
** The hashes enable an efficient, index free method of looking up data on a Tranche network
** Post download, the Tranche hash can be used to check that a file's contents haven't changed since publication
* Clear licensing terms when data is uploaded, including beta-support for
How is Tranche Different than BitTorrent
While Tranche is a P2P tool similar to BitTorrent significant changes were made so that Tranche would be appropriate for the sharing of scientific data sets, or in a broader sense, any data that requires tracking of information related to what users originally uploaded the data. Here is a short list of how Tranche is similar and different to BitTorrent.
Similarities compared to BitTorrent
*Uses P2P practices to efficient share data and scale well with large volumes of users
*Free to use and open-source
Differences compared to BitTorrent
*Licensing terms for use of data must be selected prior to upload
*Users are not anonymous. All data have signatures from the uploading users.
*Data may be revoked from the network if needed
*Individual files may be downloaded from an upload that includes multiple files, e.g. need not download the entire ZIP in order to get one file.
*Data may be passphrase protected (AES 256 encryption) for restricted access
*Primarily used for sharing scientific data. No known illicit content on the network.
Related Publications
*Archive of Tranche Presentations and Posters
*Andrews PC and Falkner JA, "Open Access to Proteomics Data: A Valuable Resource for Biology and Medicine", Journal of Proteome Research 6(6): pp 2047-2048, 2007
*Falkner JA, Hill JA, Andrews PC, "Proteomics FASTA Archive and Reference Resource", Proteomics (2008)
*Falkner JA, Andrews PC, "Publicly dissemination large amounts of proteomics data in a secure and scalable fashion", http://tranche.proteomecommons.org (in submission)
*Falkner JA, Ulintz PJ, and Andrews PC, "A Code and Data Archival and Dissemination Tool for the Proteomics Community", American Biotechnology Laboratory, Apr, 2006
An infrasound gun is a hypothetical equipment for the production of acoustic waves of high intensity with low frequencies below the human audible range (infrasound). Such acoustic waves can make humans fearful, cause internal injuries, or even kill them.
A infrasound gun would consist in principle of a long whistle (similar an organ pipe), into which compressed air is blown, generating infrasound waves of high intensity. The physical fundamentals of the function mode of an infrasound gun represent the natural frequency of firm bodies and large the resonance disaster.
Up to now it cannot be proven if an infrasound generator suitable for use as weapon was built. Infrasound guns would have enormous size; reductions of their dimensions would be difficult for physical reasons. Reports of possible incidents due to the use of infrasound waves, are therefore to be regarded at present with great care.
In a study from the year 1968 on the effects of very high sound pressures, the French researcher Vladimir Gavreau describes the effects of longer continuous high sound pressures on humans. It examined here however not infrasound, but very probably audible tones with a frequency of 196 cycles per second. At a volume of 160 decibels it describes its own impressions: "we noticed a painful resonance in the body; we had the feeling of everything vibrate in us if we spoke or us moved." Such a high sound pressure prevails a few meters from jet engines. Far assumed Gavreau that it could have caused internal bleedings, if the attempt had persisted longer than 5 minutes. It could not show a proof for such an effect however, since no such experiments had been accomplished. To publication of the scientific paper in the Science journal it came to the publication more differently sensationally opened article into daily papers over deadly effects of acoustic waves. Thus the Miami Herald wrote an article about Gavreau's article "sound ray developed as a killer", without considering the facts, with reference to the same scientist assumptions over it were later expressed that the infrasound produced by vehicles driving with open windows may be deadly.
Further, an infra sound gun is to have been developed in the Research Institute for Electroacoustics of the CNRS in Marseille under the direction of Gavreau according to different sources around 1964. Allegedly the infrasound waves of a fan in a new building of the Institute with the coworkers of symptoms such as headache, nausea, skin itching and vibration frost to have caused and to the development of several sound cannons to have in such a way inspired. On basis of this coincidental discovery equipment is to have been developed, which produced for the report after acoustic waves of 196 cycles per second and so that both to hurting and caused tear brought the gastro-intestinal tract of the coworkers in walls. A further sound cannon is to have been still larger and have worked with 37 cycles per second. Allegedly this is powerful enough to destroy buildings.
Popular culture
The Kate Bush song Experiment IV is about the testing of an intrasound weapon which goes awry, destroying its creators.
Literature
*Gavreau V., Infra Sons: Générateurs, Détecteurs, Propriétés physiques, Effets biologiques, in: Acustica, Vol .17, No. 1 (1966), S.1-10.
*Gavreau V., "Sons graves intenses et infrasons" in: Scientific Progres - la Nature (Sept. 1968) S. 336-344
A infrasound gun would consist in principle of a long whistle (similar an organ pipe), into which compressed air is blown, generating infrasound waves of high intensity. The physical fundamentals of the function mode of an infrasound gun represent the natural frequency of firm bodies and large the resonance disaster.
Up to now it cannot be proven if an infrasound generator suitable for use as weapon was built. Infrasound guns would have enormous size; reductions of their dimensions would be difficult for physical reasons. Reports of possible incidents due to the use of infrasound waves, are therefore to be regarded at present with great care.
In a study from the year 1968 on the effects of very high sound pressures, the French researcher Vladimir Gavreau describes the effects of longer continuous high sound pressures on humans. It examined here however not infrasound, but very probably audible tones with a frequency of 196 cycles per second. At a volume of 160 decibels it describes its own impressions: "we noticed a painful resonance in the body; we had the feeling of everything vibrate in us if we spoke or us moved." Such a high sound pressure prevails a few meters from jet engines. Far assumed Gavreau that it could have caused internal bleedings, if the attempt had persisted longer than 5 minutes. It could not show a proof for such an effect however, since no such experiments had been accomplished. To publication of the scientific paper in the Science journal it came to the publication more differently sensationally opened article into daily papers over deadly effects of acoustic waves. Thus the Miami Herald wrote an article about Gavreau's article "sound ray developed as a killer", without considering the facts, with reference to the same scientist assumptions over it were later expressed that the infrasound produced by vehicles driving with open windows may be deadly.
Further, an infra sound gun is to have been developed in the Research Institute for Electroacoustics of the CNRS in Marseille under the direction of Gavreau according to different sources around 1964. Allegedly the infrasound waves of a fan in a new building of the Institute with the coworkers of symptoms such as headache, nausea, skin itching and vibration frost to have caused and to the development of several sound cannons to have in such a way inspired. On basis of this coincidental discovery equipment is to have been developed, which produced for the report after acoustic waves of 196 cycles per second and so that both to hurting and caused tear brought the gastro-intestinal tract of the coworkers in walls. A further sound cannon is to have been still larger and have worked with 37 cycles per second. Allegedly this is powerful enough to destroy buildings.
Popular culture
The Kate Bush song Experiment IV is about the testing of an intrasound weapon which goes awry, destroying its creators.
Literature
*Gavreau V., Infra Sons: Générateurs, Détecteurs, Propriétés physiques, Effets biologiques, in: Acustica, Vol .17, No. 1 (1966), S.1-10.
*Gavreau V., "Sons graves intenses et infrasons" in: Scientific Progres - la Nature (Sept. 1968) S. 336-344
Bill King XVII
(Born January 12th, 1972) is an actor who has appeared in two television episodes, was the casting director for another episode, and is now fairly famous on the Facebook application Knighthood. King has an IMDb article which you can find in the external links, or by searching for Bill King XVII.
In "Bloody Valentine"(2004), an episode of "F2: Forensic Factor" on the Discovery Channel, he played the part of Eric Richardson, the lead investigator in the murder of Susan Hamilton by her husband Dr. John Hamilton. "The cry for help comes from Oklahoma City's most exclusive neighborhood. My wife's bleeding all over the place, Dr. John Baxter Hamilton tells the 911 operator. I don't know, she looks like somebody hurt her. It's Valentine's morning and socialite Susan Hamilton lies nude, smashed in a pool of blood. The science suggests a crime of heated rage and cold calculation, a killer with the intelligence to cover his trail and the composure to mask his guilt."(quoted from http://www.discoverychannel.ca/shows/episodedetails.aspx?eid27&sid25).
In "A Gem of a Heist"(2004), an episode of "Masterminds", he played the part of Mark Andrews, the jewelry store owner who got robbed by Tony Granims' team. "In 1999, Tony Granims put together a dream team that perfected the art of the jewelry store heist. The resulting rash of robberies in separate states baffled the police. The gang was so confident they often knocked off more than one store in a night. Granims, a registered jeweler ran a security alarm company for the police. He was also a registered private investigator. Who would ever suspect him?" (quoted from http://www.history.ca/ontv/titledetails.aspx?titleid=74639).
He was also the casting director for "Out There... with Melissa DiMarco"(2005), an actress / entertainment reporter's life in the industry.
In Knighthood, a Facebook application, Becky Sedlock requested that other players talk Bill King into joining under her as a 'vassal' for 24 hours, in which she would pay that player 100,000 virtual gold for doing so. Because of this request, many players who have never heard of Bill king now know a little more about him. He has received numerous messages from players, mostly offering a portion of the gold, trying to get him to become Becky's vassal. Bill King has said several times that he does not care about the gold, and is looking for more creativity from the players. King has been given an OK by his current liege, Jani Ilola, to leave him for a time to become Becky's vassal and decided to take up the offer from Andrew McCallum who suggested that they split the gold with all of the runner ups. They have given the gold out to the players, you can follow this facebook thread by searching for "Giving away 150,000 gold! This is not a joke!" on the discussion page of knighthood on facebook. You can also find another page about this entitled "If you helped me recruit Bill King, I need your link :)"
(Born January 12th, 1972) is an actor who has appeared in two television episodes, was the casting director for another episode, and is now fairly famous on the Facebook application Knighthood. King has an IMDb article which you can find in the external links, or by searching for Bill King XVII.
In "Bloody Valentine"(2004), an episode of "F2: Forensic Factor" on the Discovery Channel, he played the part of Eric Richardson, the lead investigator in the murder of Susan Hamilton by her husband Dr. John Hamilton. "The cry for help comes from Oklahoma City's most exclusive neighborhood. My wife's bleeding all over the place, Dr. John Baxter Hamilton tells the 911 operator. I don't know, she looks like somebody hurt her. It's Valentine's morning and socialite Susan Hamilton lies nude, smashed in a pool of blood. The science suggests a crime of heated rage and cold calculation, a killer with the intelligence to cover his trail and the composure to mask his guilt."(quoted from http://www.discoverychannel.ca/shows/episodedetails.aspx?eid27&sid25).
In "A Gem of a Heist"(2004), an episode of "Masterminds", he played the part of Mark Andrews, the jewelry store owner who got robbed by Tony Granims' team. "In 1999, Tony Granims put together a dream team that perfected the art of the jewelry store heist. The resulting rash of robberies in separate states baffled the police. The gang was so confident they often knocked off more than one store in a night. Granims, a registered jeweler ran a security alarm company for the police. He was also a registered private investigator. Who would ever suspect him?" (quoted from http://www.history.ca/ontv/titledetails.aspx?titleid=74639).
He was also the casting director for "Out There... with Melissa DiMarco"(2005), an actress / entertainment reporter's life in the industry.
In Knighthood, a Facebook application, Becky Sedlock requested that other players talk Bill King into joining under her as a 'vassal' for 24 hours, in which she would pay that player 100,000 virtual gold for doing so. Because of this request, many players who have never heard of Bill king now know a little more about him. He has received numerous messages from players, mostly offering a portion of the gold, trying to get him to become Becky's vassal. Bill King has said several times that he does not care about the gold, and is looking for more creativity from the players. King has been given an OK by his current liege, Jani Ilola, to leave him for a time to become Becky's vassal and decided to take up the offer from Andrew McCallum who suggested that they split the gold with all of the runner ups. They have given the gold out to the players, you can follow this facebook thread by searching for "Giving away 150,000 gold! This is not a joke!" on the discussion page of knighthood on facebook. You can also find another page about this entitled "If you helped me recruit Bill King, I need your link :)"
Steffen Christian Martin Gielen (b. 1 November, 1982), is a German theoretical physicist.
Gielen grew up in the German Land Rhineland-Palatinate in Ingelheim and Bad Kreuznach. He went to the Lina-Hilger grammar school and passed his Abitur exam in 2001. After having studied for several years at the Freie Universität Berlin he studied for one year in Cambridge, where in 2007 he won the Mayhew Prize and became a research student under the supervision of Gary Gibbons. Gielen's main interests in research are Classical and Quantum Gravity, Black Holes, and Quantum Field Theory.
Gielen grew up in the German Land Rhineland-Palatinate in Ingelheim and Bad Kreuznach. He went to the Lina-Hilger grammar school and passed his Abitur exam in 2001. After having studied for several years at the Freie Universität Berlin he studied for one year in Cambridge, where in 2007 he won the Mayhew Prize and became a research student under the supervision of Gary Gibbons. Gielen's main interests in research are Classical and Quantum Gravity, Black Holes, and Quantum Field Theory.