How do we search, store, index, annotate molecules?

[drc007]

I was thinking of building a file containing molecules and the associated biological data however I'm finding difficult to identify all the molecules that have been made on the project, whether there is a unique identifier for every molecule, and then find a link to any data that might have been generated on a molecule. I've seen various web pages that contain SMILES strings but I've no idea if these are comprehensive. Some have identifiers but I don't know if the identifier refers to the parent compound, if it changes with salt form or how we distinguish between batches of compound. How are OSM numbers assigned and how do check a compound has not been prepared before? As assay data is generated how do link this to a parent/salt form/batch and how do you decide what data can be averaged? Whilst I could plough through the web pages looking for information it would soon be out of date, so it would be better if there was a sustainable model in place for new molecules and data.

[madgpap]

Hi all, @lpatiny very nice work indeed. @mattodd ChEMBL would need to process the sdf and standardise/integrate the structures and activity values before a release so it's not ideal for instant hosting. With cheminfo though we could perhaps add a link here: https://www.ebi.ac.uk/chembl/malaria/source pointing to an up to date, cheminfo-rendered compound table + associated plots.

[drc007]

I think unless you are committed to having a person dedicated to regularly maintaining a ChEMBL update the solution @madgpap suggests would be much better and would hopefully contain all the current data. You could still submit annual snapshots to ChEMBL to include in their releases.

[mattodd]

Catching up on these inputs: 1) It seems to me that a Gdoc is a good solution at the moment. It can be edited by anyone and exported as the file needed for Cheminfo. It would be useful to have a fixed URL for the latest rendering of the latest Gdoc, e.g. an automated daily export of the Gdoc to a TDF that can be acted upon by Cheminfo. (Just to flag up - we are, overall, aiming to remove the need to curate these data manually by the way - the conversation earlier in this thread with @BillMills - i.e. have the data entered originally, in the ELN, in a way that can be used to create a file (of whatever type) that can be manipulated in this way. So the addition of Cheminfo looks like it solves the visualization issue, but we still need the automation of the master list file of all molecules)

2) It would be nice if the user can choose columns, yes. But the defaults should be

Structure Potency Code URL to summary page for the molecule [physicochem parameters] [Any other biology is less important for this file, I think, but could include later] [Strings]

i.e. this is intended as a way to see the most important SAR data in an intuitive way.

Chris - some compounds have links to summary pages. The manual nature of this has prevented it being generally done - it's very time consuming. Back to the conversation about automation. The idea is to automate the construction of those summary pages - one page for each molecule in the project (including synthetic intermediates) that includes synthetic attempts and all the biology. The entry in the table would link to that.

3) @madgpap - sounds very good, thanks. A link would be great.

Summary - at this stage it'd be good to have a browsable list of the molecules in this series with potency, structure, and a URL for more info where possible. Such a resource would be valuable as a submission along with the first Series 4 paper.

Happy to organise a TC. I can set up an Adobe Connect meeting that we could record if people would be happy to do that. No software needed.

[lpatiny]

1) It seems to me that a Gdoc is a good solution at the moment. It can be edited by anyone and exported as the file needed for Cheminfo.

Well in fact this ChemInfo view loads directly the data from GDocs. No need to export, live update. It was for this project that we first tried this approach but seems to work.

Because it seems you want to go forward in this direction I will work on a “malaria” website with different views so that we have full flexibility about how to display the data.

You may also add in the GDoc file column with IDs from which we can construct a URL. There could for for example a column DOI

And in this column you would put

10.1021/ci300563h

After I can do something to convert this to a clickable URL because I know I should just put in front

http://dx.doi.org/10.1021/ci300563h

Same can be done for pubchem links, chembl, … This would allow even to put in an IFRAME all the related information without having to leave the page like we did in the wikipedia project

http://www.cheminfo.org/wikipedia

I’m free to have a TC. I prefer Hangout allowing me to share screen. My hangout: lpatiny

[drc007]

1) It seems to me that a Gdoc is a good solution at the moment. It can be edited by anyone and exported as the file needed for Cheminfo. Well in fact this ChemInfo view loads directly the data from GDocs. No need to export, live update. It was for this project that we first tried this approach but seems to work.

This is a very important point, it means that users are always able to see live data.

Potency

I think you have to get away from this as a column header, it gives no clue to whether it is IC50, EC50, EC90, minimum inhibitory concentration, in vitro, in vivo, cell-based, biochemical screen etc. I'd suggest a minimal descriptive column header e.g. PfaI IC50 uM, and as Luc has suggested maintain another google docs spreadsheet with each row describing a particular assay, reference or page describing assay. You are unlikely to have many assays and each only needs to be added once.

This would also be very useful when it comes to uploading data to ChEMBL.

[lpatiny]

We will try to broadcast our workshop on the visualizer "live" https://plus.google.com/u/0/events/c2svl99a5vn158ob08f40id6lp8

[bkatiemills]

@drc007 @mattodd great work - the real point of the local SQL database I was recommending was to decouple data entry from data presentation, which this google docs solution also does. I would strongly encourage investigating a way to make local backups of those spreadsheets of raw data, but the design from a bird's eye view looks sound to me.

[lpatiny]

Indeed backup !!! I never lost any documents from google docs but still it is so valuable information. A crontab with a script like

https://github.com/alanctgardner/gdrive-backup-perl https://github.com/alanctgardner/gdrive-backup-perl

Should work if somebody wants to implement it.

[mattodd]

Out of interest, Chris and Luc, here's the link to the old Google Doc we kept for Series 1. It's no longer used, but illustrates where we were up to. (the project's OSM now, not osdd by the way). http://bit.ly/OSDDcompounds We could use a custom URL for the Google Doc you created, Chris. Anyone have the credentials to create "OSMCompounds" Thinking ahead, is it useful to have a separate sheet for each compound Series ("OSMCompoundsSeries4"), or would it be better to include a column in the sheet that specifies the Series a compounds belongs to?

[lpatiny]

It would be better to add a column for the series the compounds belong to otherwise we would need in order to compile a view to make many queries. Moreover we would be able to add checkbox to select with series you would like to see.

[drc007]

I'd have a single spreadsheet with a new column, you can be sure you will want to compare compounds at some point, and being able to categorise in a single plot will be very useful.

[mattodd]

OK, perfect, then let's add that column. Very useful!

On 27 April 2015 at 23:36, lpatiny notifications@github.com wrote:

It would be better to add a column for the series the compounds belong to otherwise we would need in order to compile a view to make many queries. Moreover we would be able to add checkbox to select with series you would like to see.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-96653985 .

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 | W http://opensourcemalaria.org/

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.

[drc007]

Column added.

[drc007]

The spreadsheet now includes all the "inherited" compounds.

[mattodd]

Fantastic. So the link remains

https://docs.google.com/spreadsheets/d/1Rvy6OiM291d1GN_cyT6eSw_C3lSuJ1jaR7AJa8hgGsc/edit#gid=0

Anyone have the ability to obtain the bespoke bitly URL that includes "OSMCompounds" just to make this a simpler link.

To Do: Add into the sheet all the structures on the Series 4 wiki that do not have potencies listed, which I believe is all the more recently-made compounds - those mentioned at the bottom of the wiki by name but with no associated strings. @jlee8294

[drc007]

Also I've see spreadsheets which contain a hypertext link next to the spreadsheet name. If anyone knows how to add that it would be useful to add a link to the visualisation. @lpatiny

[lpatiny]

It is now done under the ID of the first column label.

We should not add a line because it destroy the view …

[drc007]

Hi @madgpap

We are now populating the spreadsheet at https://docs.google.com/spreadsheets/d/1Rvy6OiM291d1GN_cyT6eSw_C3lSuJ1jaR7AJa8hgGsc/edit#gid=510297618

Could you have a look at it and see if there are any obvious issues that might prevent this being used to import data into ChEMBL?

[madgpap]

Hi @drc007

I cannot see any major issues. For ChEMBL upload we would also need an sd file (just connection table and compound ID - I could prepare this) and some more info on the assay (description, organism/target name, strain, organism accession, etc.)

[drc007]

Hi @madgpap,

We have a (incomplete) description of the columns here. https://docs.google.com/spreadsheets/d/1CyF9O1zu46I-l2eRgRtMK8oBZRJV2um0482j17aVIC4/edit#gid=0

If you let me know of any additional columns you would require we can add them.

[mattodd]

Hi there @lpatiny - just a couple of questions about the cheminfo link. These have come up because the main OSM landing page (i.e. opensourcemalaria.org) is being revamped a little by our web dev friends. I'd really like to include a link to the cheminfo page there, because this is so incredibly useful, so that people can easily browse the structures in the project. 1) As you said, it works on Chrome, not Firefox. Is that likely to remain the case? i.e. should we explicitly say this on the webpage ("Chrome only for now") 2) I assume it's likely not to work on mobile devices (unless those devices use Chrome?) On my Android the page appears correctly (in Chrome) but I can't scroll down the sheet, for example, and obviously the page appears as-is rather than in a mobile version, for example. 3) What are the chances (and this is not intended as a criticism!) of improved loading times? When I go to the page there is a wait of maybe 5-10 seconds while the page loads. Some visitors might get impatient and not wait. What if we mirrored the page somewhere - is that possible? Answers will feed into the current web dev wizardry being done by @chuckfitzpatricksf and others.

[madgpap]

Hi @drc007 This looks good!

[drc007]

Hi @lpatiny, @mattodd, A couple of comments, I assume the time taken load is because the data is being taken live from the google docs spreadsheet and the properties calculated. This has the advantage that the data is always up to date, if you want faster loading then you may need to have a cached copy, you would then need to decide how this would be generated, by whom, and how often.

As for the display, I'd go with the table and a 2D scatterplot.

[lpatiny]

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

[mattodd]

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this - maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034 .

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 | W http://opensourcemalaria.org/

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.

[drc007]

Hi @lpatiny, I was wondering if there was a way to open the display and highlight a specific record e.g. MMV670947? This could be a very useful way of linking compounds mentioned in other parts of the site when you can't remember the specific structure.

[drc007]

Hi @mattodd , @lpatiny , I've added another column to the spreadsheet to contain the qualifier for the Pfal result, I've also created a column called PfaI EC50 uMol (results). We need to only have numeric data in PfaI EC50 uMol (mean), so all results can go in PfaI EC50 uMol (results) and only the averaged result in "mean"

[alintheopen]

Thanks @drc007 looks good. I was talking to @mattodd today and we were once again discussing the best way to link this powerful spreadsheet to the ELN and also avoid overlap of data entry effort. This is probably a discussion for another thread and something that we could do with discussing in a meeting at some point but we also talked about a few things linked to the spreadsheet which is working really well and requires a lot less input that the system we were previously using.

I am going to contact ScienceCloud to find out the best procedure for groups outside Sydney to register compounds with MMV numbers and then write-up a 'How To' for researchers updating this spreadsheet as we need a strict protocol to keep the SS up to date. One question I have is regarding security. Currently, the Google sheet can be accessed by anyone with the link and I was wondering if we could change this so that only people adding data can edit the sheet. We looked at the revision history feature which should prevent any issues from someone accidentally overwriting data, right? Would we be able to push the data from this spreadsheet to an SDF at regular intervals so that anyone could use the SDF. Knime has workflows that can also produce tabulated data containing the structure of molecules which could be powerful feature to complement the visualisation that you have imbedded in the Google Sheet.

We were also wondering whether including strings in the G Sheet means that we can omit them from future Wiki edits as we would ultimately have a searchable database of OSM compounds for anyone to view.

There are possibly a few students joining the OSM Sydney team in July for a month or so. We're hoping that they might be interested in helping us to update sheets for all OSM compounds for all series. So, it would be good if we could decide whether we will include all compounds or just those evaluated biologically. Also, should we have one spreadsheet or divide by series?

Thanks for your thoughts!

[drc007]

@alintheopen @mattodd I think having a list of registered editors is a good idea, you should be able to change the settings (Edit:Share). Just make sure that it is possible for anyone to have read only access. It is also possible to script an automatic saving of a copy at regular intervals but I've never done that. I've taken the spreadsheet and converted it into a sdf by hand just to check it could be done, but I'm not sure of the best way to do this automatically, would you like me to ask around to see if this would be possible?

It would also be useful if someone could add the in vitro metabolism and HERG data to the spreadsheet.

[alintheopen]

Hi @drc007 I think a list of registered editors is a great idea. I currently can't change the settings without making myself unable to edit so would you be able to do this as the owner Chris? It would be great if you could ask around about an automated SDF generation. We might see if a student could add the in vitro mechanism and HERG data @mattodd? The more assay tabs we enter the more the sheet begins to look like the ChEMBL spreadsheets, do you think we should make the G sheet directly compatible @madgpap?

@PatrickThomson do you think you might have time to enter the Edinburgh data? I am seeking advice on the best way to generate MMV values, but I can also add these in later. We also need to double check that no Sydney compounds from @JoannaUbels , @tscmacdonald or myself are missing.

Thanks all.

[drc007]

Hi @alintheopen and @mattodd ,

I’ve changed the settings for the google spreadsheet.

Everyone with the link can view

Current editors are

I and the editors can add new editors.

[alintheopen]

Hi @drc007 @mattodd ...I think I need to be able to edit too! :)

[alintheopen]

Thanks Chris - got the invite :+1:

[lpatiny]

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ http://www.cheminfo.org/flavor/malaria/

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this - maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774.

[mattodd]

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this - maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605 .

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 | W http://opensourcemalaria.org/

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.

[drc007]

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this - maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423.

[lpatiny]

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain notifications@github.com wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this - maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655.

[mattodd]

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain notifications@github.com wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423 .

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114889849 .

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 | W http://opensourcemalaria.org/

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.

[lpatiny]

For me

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136 http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136

is ok

On Jun 24, 2015, at 9:42 AM, Mat Todd notifications@github.com wrote:

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain notifications@github.com wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423 .

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114889849 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114893245.

[drc007]

Now looks like I’m going to be busy all day July 1st.

You should hold the meeting anyway.

On 24 Jun 2015, at 16:01, lpatiny notifications@github.com wrote:

For me

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136 http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136

is ok

On Jun 24, 2015, at 9:42 AM, Mat Todd notifications@github.com wrote:

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain notifications@github.com wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd notifications@github.com wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423 .

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114889849 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114893245.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114899376.

[mattodd]

OK, if you're sure. Shame to miss you. Luc - Hangouts? Might be nice for others to join if interested. M

On 25 June 2015 at 03:18, Chris Swain notifications@github.com wrote:

Now looks like I’m going to be busy all day July 1st.

You should hold the meeting anyway.

On 24 Jun 2015, at 16:01, lpatiny notifications@github.com wrote:

For me

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136

is ok

On Jun 24, 2015, at 9:42 AM, Mat Todd notifications@github.com wrote:

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 <

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain <notifications@github.com

wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd < notifications@github.com> wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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

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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 | W http://opensourcemalaria.org/

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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 | W http://opensourcemalaria.org/

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[lpatiny]

Hangout is ok. My gmail username is lpatiny

On 25 Jun 2015, at 14:51 , Mat Todd notifications@github.com wrote:

OK, if you're sure. Shame to miss you. Luc - Hangouts? Might be nice for others to join if interested. M

On 25 June 2015 at 03:18, Chris Swain notifications@github.com wrote:

Now looks like I’m going to be busy all day July 1st.

You should hold the meeting anyway.

On 24 Jun 2015, at 16:01, lpatiny notifications@github.com wrote:

For me

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136 < http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136

is ok

On Jun 24, 2015, at 9:42 AM, Mat Todd notifications@github.com wrote:

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136 <

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain <notifications@github.com

wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd notifications@github.com wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd < notifications@github.com> wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny notifications@github.com wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114889849

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114893245 .

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114899376 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114946020 .

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-115241587.

[mattodd]

OK, will create and send round the link.

It might be time to think about closing this Issue and forking out to new ones for unresolved matters. Anyone object?

On 25 June 2015 at 22:54, lpatiny notifications@github.com wrote:

Hangout is ok. My gmail username is lpatiny

On 25 Jun 2015, at 14:51 , Mat Todd notifications@github.com wrote:

OK, if you're sure. Shame to miss you. Luc - Hangouts? Might be nice for others to join if interested. M

On 25 June 2015 at 03:18, Chris Swain notifications@github.com wrote:

Now looks like I’m going to be busy all day July 1st.

You should hold the meeting anyway.

On 24 Jun 2015, at 16:01, lpatiny notifications@github.com wrote:

For me

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136 <

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=11&min=0&sec=0&p1=240&p2=87&p3=136

is ok

On Jun 24, 2015, at 9:42 AM, Mat Todd notifications@github.com wrote:

9 or 10 pm in Sydney is actually easier for me than 5.

On 25 June 2015 at 00:34, lpatiny notifications@github.com wrote:

Only one green line …

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

<

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=7&day=1&hour=7&min=0&sec=0&p1=240&p2=87&p3=136

Is this ok ?

On Jun 24, 2015, at 9:13 AM, Chris Swain < notifications@github.com

wrote:

I have lots of short meetings so select your time and I’ll work around it.

On 24 Jun 2015, at 15:11, Mat Todd <notifications@github.com

wrote:

It'd be good to talk about this yes. Time comparison:

http://www.timeanddate.com/worldclock/meetingtime.html?iso=20150701&p1=240&p2=87&p3=136

I could make Sydney 9 or 10pm?

On 24 June 2015 at 23:37, lpatiny notifications@github.com wrote:

I have prepared a “flavor” on our tools that will host all the datamining tools related to the malaria project that we can provide.

The new website that you should site / point to is

http://www.cheminfo.org/flavor/malaria/ < http://www.cheminfo.org/flavor/malaria/>

If you have a small logo for the project I can put it to replace the “cheminfo” logo on the top right

Also the home page should be rewritten. Just tell me what you want to put on it.

We can have a meeting about the future tools on wednesday 1 July. I’m rather free … and I’m in Europe … so you may decide the time (but not in the middle of the night)

On 04 Jun 2015, at 15:59 , Mat Todd < notifications@github.com> wrote:

OK, fantastic, thanks guys. Yes, it'd be good to catch up on this

• maybe early July, when you've time Luc?

As part of the OSM website revamp, the designers were asking this: 1) the link we're currently using is stable - i.e. is the one we should use as a link from the landing page, right? 2) And we should at the moment include "Chrome only". 3) One of the designers had found that if he went to the page and found that nothing was loading (white space in the middle) that if he clicked on "demo" it worked. That shouldn't be needed, right? He should just wait?

On 4 June 2015 at 22:07, lpatiny < notifications@github.com> wrote:

I don’t think that the loading time is related to the dynamic loading of the data but indeed currently the visualizer itself is composed of many small files.

I can understand that the first time it is slow but I’m surprised it it still slow after.

I checked with open console to prevent any cache and it takes 8s to load the page.

Retrieve the data from google takes 500 ms.

Concerning display we should not focus on only one page but we will have many of them but as always the more important is to complete the data and the google docs.

For information we are currently working on migration of rdkit to javascript in order to have more prediction of the data

We could plan a hangout meeting to discuss about the views you would like. I can work on this the week of 1 July

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108864034

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-108907774

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114870605

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114880423

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114881655

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114889849

.

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 | W http://opensourcemalaria.org/

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114893245

.

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

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114899376

.

— Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-114946020

.

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 | W http://opensourcemalaria.org/

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. — Reply to this email directly or view it on GitHub < https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-115241587 .

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-115242962 .

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 | W http://opensourcemalaria.org/

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.