Open Source Drug Discovery - Revision history

Matthew Todd: added licence

Matthew Todd — Wed, 01 May 2013 01:37:25 GMT

added licence

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	{{OSDD}}		{{OSDD}}

-	Open Source Drug Discovery (OSDD) is the concept of drug discovery where all data and ideas are shared in real time, and anyone may participate at any level. ~~This prior disclosure means that~~ will be no patents ~~and that any technology~~ is both academically and commercially exploitable by whoever wishes to do so.	+	Open Source Drug Discovery (OSDD) is the concept of drug discovery where all data and ideas are shared in real time, and anyone may participate at any level. There will be no patents. The default licence is CC-BY-3.0. Any results are both academically and commercially exploitable by whoever wishes to do so, provided the project is cited.

	This wiki aims to be a hub for global efforts in drug discovery operating on an open source model.		This wiki aims to be a hub for global efforts in drug discovery operating on an open source model.

Paul M. Ylioja: /* Medicinal Chemistry */

Paul M. Ylioja — Tue, 14 Feb 2012 02:09:43 GMT

Medicinal Chemistry

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	* [http://www.mmv.org/ Medicines for Malaria Venture]		* [http://www.mmv.org/ Medicines for Malaria Venture]
	* [http://www.cdriindia.org/sanjay.htm Sanjay Batra] at [http://www.cdriindia.org/home.asp CDRI India]		* [http://www.cdriindia.org/sanjay.htm Sanjay Batra] at [http://www.cdriindia.org/home.asp CDRI India]
		+	* [http://www.osdd.net/ OSDD] computational project at [http://www.cdriindia.org/home.asp CDRI India]

	==== Biology ====		==== Biology ====

Paul M. Ylioja: /* Open science */

Paul M. Ylioja — Tue, 14 Feb 2012 00:16:47 GMT

Open science

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	[http://en.wikipedia.org/wiki/Open_science Open science] is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.		[http://en.wikipedia.org/wiki/Open_science Open science] is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.

-	Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a [[http://www.thesynapticleap.org/schist/projects chemical synthesis of a drug], the eventual solution was influenced by project participants as it proceeded.	+	Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a [http://www.thesynapticleap.org/schist/projects chemical synthesis of a drug], the eventual solution was influenced by project participants as it proceeded.

	=== Open Source Drug Discovery ===		=== Open Source Drug Discovery ===

Paul M. Ylioja: /* Open science */

Paul M. Ylioja — Tue, 14 Feb 2012 00:16:24 GMT

Open science

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	=== Open science ===		=== Open science ===

-	[http://en.wikipedia.org/wiki/Open_science Open science] is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.~~<br>~~	+	[http://en.wikipedia.org/wiki/Open_science Open science] is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.

	Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a [[http://www.thesynapticleap.org/schist/projects chemical synthesis of a drug], the eventual solution was influenced by project participants as it proceeded.		Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a [[http://www.thesynapticleap.org/schist/projects chemical synthesis of a drug], the eventual solution was influenced by project participants as it proceeded.

Paul M. Ylioja: /* Open science */

Paul M. Ylioja — Tue, 14 Feb 2012 00:15:49 GMT

Open science

←Older revision		Revision as of 00:15, 14 February 2012
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	=== Open science ===		=== Open science ===

-	Open science is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.<br>	+	[http://en.wikipedia.org/wiki/Open_science Open science] is the application of open source methods to science. Thus data must be released as they are acquired, and it must be possible for any reader of the data to have an impact on the project. There should be a minimisation of groups working on parts of the project in isolation and only periodically releasing data - ideally complete data release and collaboration happen in real time, to prevent duplication of effort, and to maximise useful interaction between participants.<br>

-	Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a chemical synthesis of a drug, the eventual solution was influenced by project participants as it proceeded.	+	Though there is no formal line to distinguish crowdsourced projects from open science projects, it could be argued that open science projects are mutable at every level. For example, while anyone could participate in the original Galaxyzoo project, the software, and the basic project methodology, were not open to change by those who participated. On the other hand in the Polymath project, while there was a question to answer at the outset, the direction the project took could be influenced by anyone, depending on how the project went. In the Synaptic Leap discovery of a [[http://www.thesynapticleap.org/schist/projects chemical synthesis of a drug], the eventual solution was influenced by project participants as it proceeded.

	=== Open Source Drug Discovery ===		=== Open Source Drug Discovery ===

Paul M. Ylioja: /* Open Source Software Development */ links

Paul M. Ylioja — Tue, 14 Feb 2012 00:11:53 GMT

Open Source Software Development: links

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	=== Open Source Software Development ===		=== Open Source Software Development ===

-	Open source in software development implies the project was open to anyone, and the final product emerged from a distributed team of participants. There may have been a funded kernel of work initially, but the subsequent development by the community is not explicitly funded. There are many examples of high quality, robust and widely used applications that were developed by an open source model, such as the Firefox and Chrome web browsers, the Linux operating system and the Apache web server. There are thriving open source software development communities on the web at, for example, [http://sourceforge.net/ Sourceforge] and [https://github.com/ GitHub]. Central to the operation of these sites and projects is the sharing of data and ideas in near-real time.~~<br>~~	+	[http://en.wikipedia.org/wiki/Open-source_software Open source in software development] implies the project was open to anyone, and the final product emerged from a distributed team of participants. There may have been a funded kernel of work initially, but the subsequent development by the community is not explicitly funded. There are many examples of high quality, robust and widely used applications that were developed by an open source model, such as the Firefox and Chrome web browsers, the [http://en.wikipedia.org/wiki/Linux_operating_system Linux operating system] and the [http://en.wikipedia.org/wiki/Apache_HTTP_Server Apache web server]. There are thriving open source software development communities on the web at, for example, [http://sourceforge.net/ Sourceforge] and [https://github.com/ GitHub]. Central to the operation of these sites and projects is the sharing of data and ideas in near-real time.

	=== Open data ===		=== Open data ===

Paul M. Ylioja: /* Current Participants */

Paul M. Ylioja — Mon, 13 Feb 2012 04:24:24 GMT

Current Participants

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	=== Current Participants ===		=== Current Participants ===
		+
		+	A current list of participants in Open Source Drug Discovery is maintained here. The wikipedia entry for [http://en.wikipedia.org/wiki/Open_notebook_science Open Notebook Science] maintains a list of open science practitioners in other projects and disciplines.

	==== Medicinal Chemistry ====		==== Medicinal Chemistry ====

Paul M. Ylioja: /* Open data */ link to open data wiki entry

Paul M. Ylioja — Mon, 13 Feb 2012 04:16:48 GMT

Open data: link to open data wiki entry

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	=== Open data ===		=== Open data ===

-	Many valuable initiatives advocating open data have emerged in which large datasets are deposited to assist groups of researchers (''e.g.,'' [http://pubchem.ncbi.nlm.nih.gov/ Pubchem], [https://www.ebi.ac.uk/chembldb/ ChEMBL] and [http://sagebase.org/ SAGE Bionetworks]); the [http://dx.doi.org/10.1038/nature09107 release of malaria data in 2010] falls into this class. These very important ventures employ the internet as an information resource, rather than as a means for active collaboration. For people to work together on the web, data must be freely available. Yet the posting of open data is only a necessary and not sufficient condition for open science. Open data may be used without a requirement to work with anyone. The GSK malaria data, for example, may be browsed and used by people engaged in closed, proprietary research projects - there is no obligation to enagage in an open research project.<br>	+	Many valuable initiatives advocating [http://en.wikipedia.org/wiki/Hydroacylation open data] have emerged in which large datasets are deposited to assist groups of researchers (''e.g.,'' [http://pubchem.ncbi.nlm.nih.gov/ Pubchem], [https://www.ebi.ac.uk/chembldb/ ChEMBL] and [http://sagebase.org/ SAGE Bionetworks]); the [http://dx.doi.org/10.1038/nature09107 release of malaria data in 2010] falls into this class. These very important ventures employ the internet as an information resource, rather than as a means for active collaboration. For people to work together on the web, data must be freely available. Yet the posting of open data is only a necessary and not sufficient condition for open science. Open data may be used without a requirement to work with anyone. The GSK malaria data, for example, may be browsed and used by people engaged in closed, proprietary research projects - there is no obligation to enagage in an open research project.<br>

	An important feature of open data is that it maximises re-use (or should be released in a way that permits re-use). Essentially the generator of data should avoid making assumptions about what data are good for. The data acquired by the Hubble space telescope [http://archive.stsci.edu/hst/bibliography/pubstat.html has led to more publications] by teams analysing the data than from the original teams that acquired the data.<br>		An important feature of open data is that it maximises re-use (or should be released in a way that permits re-use). Essentially the generator of data should avoid making assumptions about what data are good for. The data acquired by the Hubble space telescope [http://archive.stsci.edu/hst/bibliography/pubstat.html has led to more publications] by teams analysing the data than from the original teams that acquired the data.<br>

-	The [http://pantonprinciples.org/ Panton Principles] describe important recommendations for releasing data into the open.<br>	+	The [http://pantonprinciples.org/ Panton Principles] describe important recommendations for releasing data into the open.<br>

	=== Open Innovation and Prize-based Incentives ===		=== Open Innovation and Prize-based Incentives ===

Paul M. Ylioja: /* Current Participants */

Paul M. Ylioja — Mon, 13 Feb 2012 03:44:19 GMT

Current Participants

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	=== Current Participants ===		=== Current Participants ===

-	==== Chemistry ====	+	==== Medicinal Chemistry ====

-	*[[Todd\| Todd Group]] at the [http://sydney.edu.au/science/chemistry/ University of Sydney]	+	* [[Todd\| Todd Group]] at the [http://sydney.edu.au/science/chemistry/ University of Sydney]
-	*[http://www.cdriindia.org/sanjay.htm Sanjay Batra] at [http://www.cdriindia.org/home.asp CDRI India]	+	* [http://www.mmv.org/ Medicines for Malaria Venture]
		+	* [http://www.cdriindia.org/sanjay.htm Sanjay Batra] at [http://www.cdriindia.org/home.asp CDRI India]

	==== Biology ====		==== Biology ====

Paul M. Ylioja at 03:43, 13 February 2012

Paul M. Ylioja — Mon, 13 Feb 2012 03:43:27 GMT

←Older revision		Revision as of 03:43, 13 February 2012
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	{{OSDD}}		{{OSDD}}

-	~~A hub for global efforts in~~ drug discovery ~~operating on an open source model~~.	+	Open Source Drug Discovery (OSDD) is the concept of drug discovery where all data and ideas are shared in real time, and anyone may participate at any level. This prior disclosure means that will be no patents and that any technology is both academically and commercially exploitable by whoever wishes to do so.

-	~~Brief description of what it is. Drug~~ discovery ~~in which all data and ideas are shared in real time, and anyone may participate at any level. There will be no patents. (link to TSL) Summarise laws~~.	+	This wiki aims to be a hub for global efforts in drug discovery operating on an open source model.
-		+
-	~~Summary of groups active~~	+
-		+
-	~~What can I do?~~	+

	== OSDD ==		== OSDD ==
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	Open work cannot be patented, since there can be no delays to release of data, and no partial buy-ins. If a group opts out of the project to pursue a "fork", they leave the project. Open source drug discovery must operate without patents. The hypothesis is that through working in an open mode, research and development costs are reduced, and research is accelerated. This offsets the lack of capital support for the project. Costs of clinical trials and product registration would have to be sourced from governments and NGOs. Whether this is possible is one of the central questions of OSDD.<br>		Open work cannot be patented, since there can be no delays to release of data, and no partial buy-ins. If a group opts out of the project to pursue a "fork", they leave the project. Open source drug discovery must operate without patents. The hypothesis is that through working in an open mode, research and development costs are reduced, and research is accelerated. This offsets the lack of capital support for the project. Costs of clinical trials and product registration would have to be sourced from governments and NGOs. Whether this is possible is one of the central questions of OSDD.<br>

-	=== What Can I Do? ===	+	== What Can I Do? ==

	Open projects rely on participation by interested strangers. To participate, find coordination pages of the projects, read and ask questions. Follow feeds from projects. If things aren't clear, try to contact someone involved with the project. Some sites, like this one, are wikis, and so you can edit those pages directly. Some are blogs, and so you can leave comments.		Open projects rely on participation by interested strangers. To participate, find coordination pages of the projects, read and ask questions. Follow feeds from projects. If things aren't clear, try to contact someone involved with the project. Some sites, like this one, are wikis, and so you can edit those pages directly. Some are blogs, and so you can leave comments.

	This wiki hosts current [[OSDD:Projects\|projects]]		This wiki hosts current [[OSDD:Projects\|projects]]
		+
		+	=== Current Participants ===
		+
		+	==== Chemistry ====
		+
		+	*[[Todd\| Todd Group]] at the [http://sydney.edu.au/science/chemistry/ University of Sydney]
		+	*[http://www.cdriindia.org/sanjay.htm Sanjay Batra] at [http://www.cdriindia.org/home.asp CDRI India]
		+
		+	==== Biology ====
		+
		+	* [http://www.discoverybiology.org/team/vicky-avery Avery Group] at Discovery Biology, Griffith University
		+	* [http://www.bio21.org/group-leaders/bio-chemistry/stuart-ralph Ralph Group], Bio21, Melbourne
		+	* [http://www.openlabfoundation.org/gsk.aspx GSK Tres Cantos], Spain