Update landing page reference to wiki

[mattodd]

I'm still getting feedback that scientists are unclear how to find more info about the project from the landing page. I think the structure is right, and that the status needs to be clearly described on the wiki, but perhaps the link in that direction is not 100% clear. So, @chuckfitzpatricksf , is there a way we can do the following: On the landing page, there is the little panel that pops up when you click "about". At the end of that, can we add the words "Check out where the science is up to." with the words "where the science is up to" linking to http://openwetware.org/wiki/OpenSourceMalaria

Hopefully you have time for this and it's not too irritating.

[murrayfold]

As someone who's not actively working on the project but still interested in it, I find it hard to know exactly what's happening.

I think a simple page of what's on the "to do list" would be useful. Minimal words and just a scheme of 10 or so compounds. It could maybe even be colour coded.

Red - needed but synthesis not stared Amber - synthesis underway Green - made, characterised and ready for testing

For example, when it came to voting on the next set of compounds to make, I had no easy way of telling what had been made in the last 3-4 months (without going through all the experiments in the eln).

[mattodd]

Yes, this would be good. The issue is how to do that without making it another onerous task. One way would be to have a live Chemdraw file, or rather a Marvin Sketch window, where molecules could be changed/removed etc. A more immediate solution is to increase the granularity of the Github To Do list - have individual molecules on there as separate issues, coded by labels of exactly the kind you were saying. This would allow a) filtering by whether they are being made, and b) inclusion of links about those molecules, e.g. the ELN entry where they are being made. Updates would then involve those Issues either having their labels changed (red to amber) or being closed (when complete).

On 7 October 2013 23:29, Murray Robertson notifications@github.com wrote:

As someone who's not actively working on the project but still interested in it, I find it hard to know exactly what's happening.

I think a simple page of what's on the "to do list" would be useful. Minimal words and just a scheme of 10 or so compounds. It could maybe even be colour coded.

Red - needed but synthesis not stared Amber - synthesis underway Green - made, characterised and ready for testing

For example, when it came to voting on the next set of compounds to make, I had no easy way of telling what had been made in the last 3-4 months (without going through all the experiments in the eln).

— Reply to this email directly or view it on GitHubhttps://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/92#issuecomment-25804361 .

MATTHEW TODD | Senior Lecturer and Honours Coordinator School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY Rm 519, F11 | The University of Sydney | NSW | 2006 T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104 E matthew.todd@sydney.edu.au | W http://sydney.edu.au/science/chemistry/research/todd.html

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[cdsouthan]

Good ideas, but add Blue - has results. Also try to get the InChIKeys surfaced in a Google-scraped instance for all four. Given the hours of sweat and tears going into synthesis try to convince the gang not to see the miniscule time needed to establish, maintain and update the data organising andsharing structure as onerous.

[alintheopen]

Hi all, I agree that the GitHub feed does rather dominate the landing page and could be a little confusing for those who are not already involved in the project. The Wiki could do with being more obvious, agreed - a simple way of doing this would be to change the logo (it is very faint and hard to see) so that it is inverted - white picture on blue button background or even on red. I like @murrayfold and @mattodd's suggestion I just also share concern about how much work this would mean for @chuckfitzpatricksf. In answer to your point @cdsouthan, I agree with you but I really feel that we need to find a way to automate this process from labtrove. I'm sure George would suggest Knime as a solution for this problem and I think we should probably move to maintaining several SD files that automatically extract InChi key and therefore all structural/string information from the ELN. I would suggest maintaining a separate SD file for each series which lists all compounds synthesised with ELN links and then an additional SD file that is just for OSM compounds (i.e. compounds that have biological data). Is there a way we could do this without me having to spend time copying and pasting (or even worse drawing out structures)? I'm willing to start a manual version for S4 as an experiment if someone suggests a format, but for previous entries I think we have to think of a way to automate this process. We need to have a way to neatly send all of our data to any collaborator/ChEMBL deposition.

Cheers Alice

[murrayfold]

It's easy to just maintain one SDF file and have knime filter it into different files.

I don't use knime any more, but I can set this up to create the files to get you going

[alintheopen]

OK, cool Murray. I think I can do it too I'm just unsure about the best place to host the original SD file. You know how we were using DS to visualise the data, I think we might need to switch to Marvin Sketch but the output table isn't quite as good. I need to play with this a bit but I haven't got time right now.

[cdsouthan]

Obviously a single set of SD masterfiles is the best solution. You can replicate and spawn submissions or anything else from it and you can also add metadata such as the "traffic light" colour, assay results other identifiers into it. Knime/ChemAxon sounds a good combination. JFTR could/did the breifing document authors send you an SD file?

[alintheopen]

Cheers @cdsouthan, so far we don't have an SD file for S4. We have requested but need to find out if this file exists.

[chuckfitzpatricksf]

Hi Alice and Mat,

I am on vacation until Wednesday and will look at this when I get back.

Chuck

Sent from a device with a tiny keyboard and aggressive auto-correction algorithms. Please excuse any weirdness due to those factors.

On Oct 8, 2013, at 1:04 AM, alintheopen notifications@github.com wrote:

Hi all, I agree that the GitHub feed does rather dominate the landing page and could be a little confusing for those who are not already involved in the project. The Wiki could do with being more obvious, agreed - a simple way of doing this would be to change the logo (it is very faint and hard to see) so that it is inverted - white picture on blue button background or even on red. I like @murrayfold and @mattodd's suggestion I just also share concern about how much work this would mean for @chuckfitzpatricksf. In answer to your point @cdsouthan, I agree with you but I really feel that we need to find a way to automate this process from labtrove. I'm sure George would suggest Knime as a solution for this problem and I think we should probably move to maintaining several SD files that automatically extract InChi key and therefore all structural/string information from the ELN. I would suggest maintaining a separate SD file for each series which lists all compounds synthesised with ELN links and then an additional SD file that is just for OSM compounds (i.e. compounds that have biological data). Is there a way we could do this without me having to spend time copying and pasting (or even worse drawing out structures)? I'm willing to start a manual version for S4 as an experiment if someone suggests a format, but for previous entries I think we have to think of a way to automate this process. We need to have a way to neatly send all of our data to any collaborator/ChEMBL deposition.

Cheers Alice

— Reply to this email directly or view it on GitHub.

[newgitontheblock]

This is a test to show how to use GitHub for OSM.

[alintheopen]

Now I can assign tasks to @mattodd or @newgitontheblock for example. This comment will be emailed to all watching this repo. (apologies for any spam everybody)

[chuckfitzpatricksf]

Hi, I just got free from an intense project and finally got to this minor request

So, @chuckfitzpatricksf , is there a way we can do the following: On the landing page, there is the little panel that pops up when you click "about". At the end of that, can we add the words "Check out where the science is up to." with the words "where the science is up to" linking to http://openwetware.org/wiki/OpenSourceMalaria

The change is now live on the site. Sorry for the delay.

[mattodd]

Great, thanks, Chuck.

Would you, in theory, be available for an open project meeting soon aimed at identifying how to solve some recurrent issues with the websites? Not technical things, but changes in response to user feedback? I'm thinking of calling such a meeting in the next few weeks, and bringing in anyone with an interest in how the project could work, from a non-science perspective. We often talk about usability during the science meetings, but it's usually quite brief. We need a focussed get-together of people with relevant expertise. If obvious jobs are identified that need doing, and if those jobs are major, then we could contemplate paying for such essential work

More soon, but in the meantime Happy New Year, Chuck.

On 21 December 2013 09:53, chuckfitzpatricksf notifications@github.comwrote:

Hi, I just got free form an intense project and finally got to this minor request

So, @chuckfitzpatricksf https://github.com/chuckfitzpatricksf , is there a way we can do the following: On the landing page, there is the little panel that pops up when you click "about". At the end of that, can we add the words "Check out where the science is up to." with the words "where the science is up to" linking to http://openwetware.org/wiki/OpenSourceMalaria

The change is now live on the site. Sorry for the delay.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/92#issuecomment-31047827 .

MATTHEW TODD | Associate Professor School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY Rm 519, F11 | The University of Sydney | NSW | 2006 T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104 E matthew.todd@sydney.edu.au | W http://sydney.edu.au/science/chemistry/research/todd.html

CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments.

[mattodd]

Closing this issue because we will discuss various aspects of the website (whether we can alter the "about" text, and how best to disseminate new activity about the project) in the online meeting planned for early Feb. http://malaria.ourexperiment.org/osddmalaria_meeting_/8562