OpenSourceMalaria:Technical Operations: Difference between revisions

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== Main website ==
== Main website ==


The main website for the project can be found [http://opensourcemalaria.org/ here]. The project activity is pulled directly from the OSM Github organisation.
The main landing page for the project can be found [http://opensourcemalaria.org/ here]. The project activity is pulled directly from other sites.
The [http://github.com/OpenSourceMalaria/OSM_Website_Code source] for the site is also available, the pulling activity uses Ruby/Sinatra.  


== Lab notebook ==
A guide to getting started as a contributor can be found [http://malaria.ourexperiment.org/osm_logos_and_templ/8488 here]. The various platforms used are also summarised below.
 
Molecules already entered into ChEMBL may be browsed on [https://www.ebi.ac.uk/chembl/malaria/source ChEMBL's page for the project].
 
The [http://github.com/OpenSourceMalaria/OSM_Website_Code source] for the landing page is also available if needed; the pulling activity uses Ruby/Sinatra.
 
== Lab Notebook ==


Users use the open source lab notebook [http://www.labtrove.org/ Labtrove] (previously Lablog) a PHP web application developed by the University of Southampton. Currently the primary malaria blogs run on [http://malaria.ourexperiment.org/ malaria.ourexperiment.org] on a Debian server at the University of Southampton.
Users use the open source lab notebook [http://www.labtrove.org/ Labtrove] (previously Lablog) a PHP web application developed by the University of Southampton. Currently the primary malaria blogs run on [http://malaria.ourexperiment.org/ malaria.ourexperiment.org] on a Debian server at the University of Southampton.


== Odd jobs ==
How To:
* [http://malaria.ourexperiment.org/osm_logos_and_templ/7773 Write a General Entry]
* [http://malaria.ourexperiment.org/osm_logos_and_templ/7788 Write the Perfect Chemistry Entry]
* [http://malaria.ourexperiment.org/osm_logos_and_templ/7789 Write the Perfect Biology Entry]
* [http://malaria.ourexperiment.org/osm_logos_and_templ/8576 Use the ELN to the Maximum Effect]
* [http://malaria.ourexperiment.org/osm_logos_and_templ/8913 The OSM Compound Registration System] - Related: [http://malaria.ourexperiment.org/osm_logos_and_templ/10938 How to Give Compounds MMV Numbers]
 
==Molecule Visualisation==
 
How best to visualise the molecules in OSM has been discussed several times (Github issues [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/128 128], [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/112 112] and [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/99 99]). Current protocol is to develop a means to upload to ChEMBL automatically so the molecules appear on the [https://www.ebi.ac.uk/chembl/malaria/source open drug discovery page]. The central repository of the molecules is the SD file, but the repository of details for each OSM compound may be found in the [http://malaria.ourexperiment.org/osm_procedures/group/Compound%20List Experimental Procedures page]. A possible solution is [http://www.openmolecules.org/datawarrior/ DataWarrior].
 
More than one cheminformatics string for each molecule in OSM should be included to ensure some redundancy in searches, e.g. to get over any issues arising from implicit vs explicit H and tautomers (GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/230 230] and [https://plus.google.com/u/0/+MatthewTodd/posts/Lb14nGpFmdb this post])
 
== Odd Jobs ==


For random jobs where we require hosting/a bit of compute the tendency is to use [http://nectar.org.au Nectar], a cloud based provider for academic and research institutions in Australia. It provides two free instances to researchers with reasonable enough specs that they can be used for most jobs. Debian or Ubuntu is typically the flavour of choice, but Nectar provides a wide range of images and snapshots including versions of Scientific Linux.
For random jobs where we require hosting/a bit of compute the tendency is to use [http://nectar.org.au Nectar], a cloud based provider for academic and research institutions in Australia. It provides two free instances to researchers with reasonable enough specs that they can be used for most jobs. Debian or Ubuntu is typically the flavour of choice, but Nectar provides a wide range of images and snapshots including versions of Scientific Linux.
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There are several different means used for communication, with email being the least favoured (due to a lack of openness).
There are several different means used for communication, with email being the least favoured (due to a lack of openness).


OSM has a [http://twitter.com/O_S_M Twitter] account, as well as a [http://plus.google.com/u/0/114702323662314783325/posts Google+] account.
OSM has a [http://twitter.com/O_S_M Twitter] account, a [http://plus.google.com/u/0/114702323662314783325/posts Google+] account and a [https://www.facebook.com/OpenSourceMalaria Facebook page]. In addition [http://www.youtube.com/user/OSDDMalaria Youtube] account is used to post the recorded videos of meetings.
In addition [http://www.youtube.com/user/OSDDMalaria Youtube] account is used to post the recorded videos of meetings.
 
The primary means of communicating issues requiring action/input (admininstration, science or technical) is on [http://github.com/opensourcemalaria Github].
 
For news, the project has used [http://malaria.ourexperiment.org/the_osm_blog/9739/OSM_Newsletter_1.html old-school PDF-based newsletters] to reach people unfamiliar with the platforms above, though an email-based newsletter [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/159 has been discussed].


The primary means of communicating issues including admin, chemistry and technical related queries is the [http://github.com/opensourcemalaria Github] account.
'''Publicity''' is important for the project to attract new inputs. Google ranking was assessed and could be improved (GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/231 231]) and a [http://malaria.ourexperiment.org/osddmalaria_meeting_/8562/OSM_Web_DesignPlatform_Meeting.html meeting was held] to address a number of website-related issues. Related: GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/64 64]
The current todo list, tagged with the category of issue it relates to can be found on the 'Issues' tab of the [http://github.com/OpenSourceMalaria/OSM_To_Do_List OSM to do list repo].


== Github ==
== Github ==


Almost all code and data is resident on one of the Github repositories for the OpenSourceMalaria organisation account. If the data you are looking for cannot be found there, or you are looking for experimental data the best place to probably look is the Labtrove blog. If you still are unable to find something, post an issue on the Github todo list and someone can attempt to address the issue.
Github is used for project management - a place to keep the [http://github.com/OpenSourceMalaria/OSM_To_Do_List To Do list]. Tasks are called "Issues" and may be assigned a person responsible, a deadline and some tags to allow active items to be grouped. When a task is complete, it can be closed.
 
* [http://malaria.ourexperiment.org/osm_logos_and_templ/8074 How to get started on Github]
* [http://malaria.ourexperiment.org/osm_logos_and_templ/8576 How to use Github to the maximum effect in the OSM project]
 
Almost all code and data for the OpenSourceMalaria organisation account (and landing page website) is resident on one of the Github repositories. The main .sd file of all compounds, for example, is kept there. All other experimental data will be on the electronic lab notebook, or summarised on the wiki.
 
If you still are unable to find something, post an issue on the Github Issues (to do) list and tag it with "Administration" and "question".


== Online Meetings ==
== Online Meetings ==

Revision as of 13:46, 25 August 2014

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This provides an outline of the technical and development operations for the Open Source Malaria (OSM) project.

This document is intended to provide an outline of the technical and development operations for the Open Source Malaria (OSM) project. It also includes some related information about social media accounts.

Main website

The main landing page for the project can be found here. The project activity is pulled directly from other sites.

A guide to getting started as a contributor can be found here. The various platforms used are also summarised below.

Molecules already entered into ChEMBL may be browsed on ChEMBL's page for the project.

The source for the landing page is also available if needed; the pulling activity uses Ruby/Sinatra.

Lab Notebook

Users use the open source lab notebook Labtrove (previously Lablog) a PHP web application developed by the University of Southampton. Currently the primary malaria blogs run on malaria.ourexperiment.org on a Debian server at the University of Southampton.

How To:

Molecule Visualisation

How best to visualise the molecules in OSM has been discussed several times (Github issues 128, 112 and 99). Current protocol is to develop a means to upload to ChEMBL automatically so the molecules appear on the open drug discovery page. The central repository of the molecules is the SD file, but the repository of details for each OSM compound may be found in the Experimental Procedures page. A possible solution is DataWarrior.

More than one cheminformatics string for each molecule in OSM should be included to ensure some redundancy in searches, e.g. to get over any issues arising from implicit vs explicit H and tautomers (GHI 230 and this post)

Odd Jobs

For random jobs where we require hosting/a bit of compute the tendency is to use Nectar, a cloud based provider for academic and research institutions in Australia. It provides two free instances to researchers with reasonable enough specs that they can be used for most jobs. Debian or Ubuntu is typically the flavour of choice, but Nectar provides a wide range of images and snapshots including versions of Scientific Linux. For jobs which may require significantly more processing we may rely instead upon EC2 instances.

Communication

There are several different means used for communication, with email being the least favoured (due to a lack of openness).

OSM has a Twitter account, a Google+ account and a Facebook page. In addition Youtube account is used to post the recorded videos of meetings.

The primary means of communicating issues requiring action/input (admininstration, science or technical) is on Github.

For news, the project has used old-school PDF-based newsletters to reach people unfamiliar with the platforms above, though an email-based newsletter has been discussed.

Publicity is important for the project to attract new inputs. Google ranking was assessed and could be improved (GHI 231) and a meeting was held to address a number of website-related issues. Related: GHI 64

Github

Github is used for project management - a place to keep the To Do list. Tasks are called "Issues" and may be assigned a person responsible, a deadline and some tags to allow active items to be grouped. When a task is complete, it can be closed.

Almost all code and data for the OpenSourceMalaria organisation account (and landing page website) is resident on one of the Github repositories. The main .sd file of all compounds, for example, is kept there. All other experimental data will be on the electronic lab notebook, or summarised on the wiki.

If you still are unable to find something, post an issue on the Github Issues (to do) list and tag it with "Administration" and "question".

Online Meetings

Online meetings use Adobe Connect provided and hosted by the University of Sydney. As with everything else, these meetings are open to everyone and each meeting is recorded and subsequently uploaded to the OSM youtube account.


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