OpenSourceMalaria

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{{OpenSourceMalaria}}
{{OpenSourceMalaria}}
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Open Source Malaria (OSM, pronounced "''awesome''") is aimed at finding new medicines for malaria using strictly open source principles, embodied in the [[Open_Source_Research | 6 Laws of Open Research]].
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[http://opensourcemalaria.org/ Open Source Malaria (OSM)] is aimed at finding new medicines for malaria using open source principles, embodied in the [[Open_Source_Research | 6 Laws of Open Research]]. At the moment the majority of work involves the synthesis of analogs of compounds identified by big pharma, with the aim of improving their potency while making the molecules more "druggable", what is known as a "hit-to-lead" campaign.
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This wiki describes where the project is up to, and summaries of relevant data. For other aspects of the project, see the main [http://opensourcemalaria.org/# Project Landing Page].
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Medicinal chemists should head to the [[OpenSourceMalaria:Story_so_far|project summary]], then the [[OpenSourceMalaria:Compound_Series| individual compound series page]]. The most active series at the moment is [[OpenSourceMalaria:Triazolopyrazine_(TP)_Series|Series 4]].
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If you would like to improve these wiki pages, you will need to get an OpenWetWare account ([[OpenWetWare:How_to_join |which is easy]]).
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For a good general overview, see the '''April 2014 newsletter''', which can be downloaded as a PDF [http://malaria.ourexperiment.org/data/files/10840/OSM%20Newsletter%20April%202014.pdf here].
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== About the Malaria Project ==
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This wiki describes where the project is up to, and archives some data and loose ends. For everything else about the project, see the main [http://opensourcemalaria.org/# Project Landing Page]. For a list of current to do items that can be filtered by type and series, see the [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?state=open To Do List].
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A human-friendly summary of the science to date can be found in [[OpenSourceMalaria:Story_so_far|'''The Story So Far''']].
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==About OSM, What's Needed and how to Contact==
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A description of what open research is can be found in the [[Open_Source_Research|'''Open Research Page''']]
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The background to the project may be found in the [[OpenSourceMalaria:Story_so_far|Story so Far]]. Publications from the project and other outputs are in the [[OpenSourceMalaria:Links|'''Links''']] page, along with media about the project.
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Aggregated data on various branches of the project so far can be found on the [[OpenSourceMalaria:Compound_Series|Compound Series Page]].
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The main resources needed in the OSM project are '''experimental input''', particularly [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=Being+Synthesised+Now&page=1&state=open chemical compound synthesis] and help with chem/bioinformatics. Anyone can make compounds, get them tested and contribute data. You don't have to be a research scientist - maybe you're an undergrad doing a lab.
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== What's Happening and What's Needed ==
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If you have no access to a lab, there are a number of important other things needed, labelled as such on the To Do List, such as things to do with [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=Writing&milestone=&page=1&state=open writing] or [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=PR&milestone=&page=1&state=open PR] to help spread the word.
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Daily updates (including the To Do list) can be accessed through [http://opensourcemalaria.org/# the project's main hub].
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Ideally everything happens in the public domain through any of the ways shown on the [http://opensourcemalaria.org/# Landing Page] but you can in the last resort contact the consortium using opensourcemalaria@gmail.com
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At the moment (July 2013) there is most activity on [[OpenSourceMalaria:GSK_Amino-thienopyrimidine_Series|'''Series 2''']], with the raw data in [http://malaria.ourexperiment.org/aminotpseries this lab notebook].
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==Help Maintain this Wiki==
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The main resource needed in the OSM project is '''experimental input''', particularly chemical compound synthesis. Anyone can make compounds, get them tested and contribute data. You don't have to be a research scientist - maybe you're an undergrad doing a lab.
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If you would like to improve these wiki pages, you will just need to get an OpenWetWare account ([[OpenWetWare:How_to_join |which is easy]]).
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If you have no access to a lab, there are a number of important admin things needed, labelled as such on the [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?state=open To Do List].
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==Open Source Drug Discovery More Generally==
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A [http://openwetware.org/wiki/OSDDMalaria:OSDD_Malaria_Meeting_Sydney_2012 one-day meeting on open source drug discovery for malaria] was held in February 2012. General issues surrounding the feasibility of open source drug discovery were discussed, followed by more specific malaria-related ideas. These talks are gradually [http://www.youtube.com/playlist?list=PL84A4E62C3C72863D going up on YouTube] with [http://www.thesynapticleap.org/node/390 annotations], and they frame many of the relevant issues, for example the landscape of drug discovery in neglected diseases, and whether patents are necessary in drug discovery. An important message is that open ''source'' drug discovery is where anyone may participate in driving the research, which is different from a more general use of the word "open" where data are made freely available, but perhaps after a delay which essentially prevents participation by others.
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==How We Run the Project==
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The way the project is run is one of the novelties, though as with everything in this project nothing is static and advice is always welcome on improvements. Raw experimental data are recorded in an online, openly-readable [http://malaria.ourexperiment.org/ electronic lab notebook]. [http://www.thesynapticleap.org/malaria/community The Synaptic Leap] is being used to discuss ideas and results, as well as plan future work. The project's [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts Google+ page] is a light way to keep up with developments and discuss. The project's [https://twitter.com/#!/OSDDMalaria Twitter feed] is a broadcast mechanism for updates. LinkedIn as used in the past on another project as a way of connecting with relevant experts, but has not been used much so far in this project. A [http://openwetware.org/wiki/Open_Source_Drug_Discovery_-_Malaria wiki] (that includes this page) is used to host the current overall project status. Updates on the project's progress can also be found at our  [http://www.facebook.com/OSDDforMalaria Facebook page], and this also a place for interaction. If you wish to participate in this project, you can sign up to all these sites, and you would then be sent the Twitter/G+ passwords so you can used the same accounts.
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==Why Take Part?==
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What of motivations? Why would people want to contribute to this project? Partly to solve a problem. Partly to be involved with quality science that is open, and hence subject to the most brutal form of ongoing peer-review. Partly for academic credentials since regular peer-reviewed papers will come from the project. Partly to demonstrate competence publicly - open science is meritocratic and status-blind. Perhaps a mixture of all these things.
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A competition is possible in the future, i.e. with a cash prize. Progress towards a very promising lead compound series has been rapid, but there is a long road to a compound that looks sufficiently promising that it moves towards clinical trials. There's a lot of tweaking needed, and perhaps even the move to another series. It is not obvious what will happen. It is certain the project will need a lot more input than it has received to date. A prize may increase traffic and input. The competition would be teamless, however, awarded based on performance of individuals within a group where everything is shared. Not sharing data or ideas leads to disqualification. Such a competition is difficult to judge, difficult to award, and hence almost certainly worth doing. More about this is [http://intermolecular.wordpress.com/2011/11/13/open-science-funding-government-grants-and-cash-incentives/ here].
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==Ownership==
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A final point - the project is open. Nobody owns it. Those people most active in the project lead it while they are active. If you wish to contribute, in any capacity, please do so. There is no need to "clear" anything with existing project members by email first. To date is has been very common for current participants to receive questions/suggestions from people by email, which is to be discouraged. In the development of Linux, the need for Linus Torvalds to approve everything caused a serious bottleneck, and the observation that "Linus doesn't scale". ''Nobody scales, but the team does''. So it's more efficient if all the project discussions are held publicly. Many people do not like this idea. In science the idea of "beta testing" something is alien. When data are released in science there is an expectation that the data are correct, and essentially finished. This project eschews this view. All data are released immediately, all discussions are public, anyone can participate.
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== Discussion ==
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This is a wiki, meaning it's meant as a site for how projects are going. For discussion try [http://www.thesynapticleap.org/malaria/community The Synaptic Leap], or the project's [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts Google+ page], and for updates try the [http://twitter.com/#!/osddmalaria Twitter feed] and [http://www.facebook.com/OSDDforMalaria Facebook Page]. If you would like access to the Twitter or G+ accounts because you've become a member of the project please email OSDD.Malaria@gmail.com.
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Relevant papers are available in the [http://www.mendeley.com/groups/1846251/osddmalaria/ Mendeley group], to which anyone can add.
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==Licence==
==Licence==
The OSM project's licence unless otherwise stated is [http://creativecommons.org/licenses/by/3.0/ CC-BY-3.0] meaning you can use whatever you want for whatever purpose, provided you cite the project.
The OSM project's licence unless otherwise stated is [http://creativecommons.org/licenses/by/3.0/ CC-BY-3.0] meaning you can use whatever you want for whatever purpose, provided you cite the project.

Current revision

Malaria Home        OSM So Far        Compound Series        Links        Open Source Research Home        Technical Operations       


Open Source Malaria (OSM) is aimed at finding new medicines for malaria using open source principles, embodied in the 6 Laws of Open Research. At the moment the majority of work involves the synthesis of analogs of compounds identified by big pharma, with the aim of improving their potency while making the molecules more "druggable", what is known as a "hit-to-lead" campaign.

Medicinal chemists should head to the project summary, then the individual compound series page. The most active series at the moment is Series 4.

For a good general overview, see the April 2014 newsletter, which can be downloaded as a PDF here.

This wiki describes where the project is up to, and archives some data and loose ends. For everything else about the project, see the main Project Landing Page. For a list of current to do items that can be filtered by type and series, see the To Do List.

About OSM, What's Needed and how to Contact

The background to the project may be found in the Story so Far. Publications from the project and other outputs are in the Links page, along with media about the project.

The main resources needed in the OSM project are experimental input, particularly chemical compound synthesis and help with chem/bioinformatics. Anyone can make compounds, get them tested and contribute data. You don't have to be a research scientist - maybe you're an undergrad doing a lab.

If you have no access to a lab, there are a number of important other things needed, labelled as such on the To Do List, such as things to do with writing or PR to help spread the word.

Ideally everything happens in the public domain through any of the ways shown on the Landing Page but you can in the last resort contact the consortium using opensourcemalaria@gmail.com

Help Maintain this Wiki

If you would like to improve these wiki pages, you will just need to get an OpenWetWare account (which is easy).

Licence

The OSM project's licence unless otherwise stated is CC-BY-3.0 meaning you can use whatever you want for whatever purpose, provided you cite the project.

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