Massachusetts College of Pharmacy and Health Sciences Join OSM

alintheopen commented 9 years ago

This thread is for project planning for MCPHS. @MedChemProf is planning to conduct to UG projects next semester.

We need to identify appropriate targets and share ELN links that will be helpful for the project. First meeting scheduled for w/b 02.11.15.

Suggested time 9.30 am Sydney time Thursday 5th November - does this work for everyone?

MedChemProf commented 9 years ago

Would it be possible to move it to 9:30 am Sydney time on Friday 5th November?

mattodd commented 9 years ago

Fine by me. Times:

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=11&day=5&hour=22&min=30&sec=0&p1=240&p2=43&p3=136&iv=1800

alintheopen commented 9 years ago

also fine with me

On Sun, Nov 1, 2015 at 10:42 PM, Mat Todd notifications@github.com wrote:

Fine by me. Times:

http://www.timeanddate.com/worldclock/meetingdetails.html?year=2015&month=11&day=5&hour=22&min=30&sec=0&p1=240&p2=43&p3=136&iv=1800

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-152820745 .

MedChemProf commented 9 years ago

I think I created the Google Hangouts event correctly. Link is https://calendar.google.com/calendar/event?action=TEMPLATE&tmeid=N2FiY3VtMzlxb3M1cmNrZm00ZWJpOXY0YXMgbWVkY2hlbXByb2ZAbQ&tmsrc=medchemprof%40gmail.com

alintheopen commented 9 years ago

Some points of disccussion for the meeting. Here are compounds we have ready/nearly ready to send and then compounds that we would like to make. Any further input welcome! november compounds

alintheopen commented 9 years ago

Also still looking for the oxetane as referenced in #292

mattodd commented 9 years ago

Great, thanks Alice. Looking forward to the discussion tomorrow morning (our time), after which we'll firm up plans for who is doing what, and which compounds are priorities. Thanks for setting up the Hangout, Chase.

MedChemProf commented 9 years ago

Just some thoughts on some structures for the meeting. Maybe be easier to refer to pictures in hand. I did not include any of the Daraprim analogs, but I was not sure where that particular part of the project stood. Looking forward to speaking with everyone later.

osm series 4 scaffold changes hangout

alintheopen commented 9 years ago

also suggested following AZ meeting. @MJTarnowski

MedChemProf commented 9 years ago

https://hangouts.google.com/call/pppj5maqqvn7tybnqlqefy6fhma

MedChemProf commented 9 years ago

@alintheopen @mattodd The link to our electronic lab notebook for the project is https://mynotebook.labarchives.com/share/MCPHS%2520MedChem/MzUxLjB8MzY3Ny8yNzAvVHJlZU5vZGUvNDA0ODg3Njc4OHw4OTEuMA==

We are still waiting for some of the mass spec data for a few of the reactions and the last is still in progress. We will update as progress is made.

mattodd commented 9 years ago

Oh, great, that's fantastic, Chase. Here's a situation where different teams are working on related/the same molecules in two different lab notebooks in the open. I'm struck by how important it is that we can aggregate related chemistry - to be able to find all the examples of a given reaction, so we can learn from each other. A first step is to make sure these intermediates have OSM numbers (do they already @alintheopen?) and then I guess the second step is to correlate the chemist codes with the OSM numbers in the Master List, but we will soon get back to this conversation we have off and on about a synthetic chemistry database, beyond the biological activity database. In short: how do we gather together, most efficiently and in the most automated fashion, all the attempts at the synthesis of a given molecule?

On 10 November 2015 at 03:35, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen @mattodd https://github.com/mattodd The link to our electronic lab notebook for the project is https://mynotebook.labarchives.com/share/MCPHS%2520MedChem/MzUxLjB8MzY3Ny8yNzAvVHJlZU5vZGUvNDA0ODg3Njc4OHw4OTEuMA==

We are still waiting for some of the mass spec data for a few of the reactions and the last is still in progress. We will update as progress is made.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-155116365 .

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

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.

alintheopen commented 9 years ago

Hi @mattodd and @MedChemProf

The compounds made to date have OSM-S numbers. @MedChemProf if your team make anything that hasn't already been made by the project then you should give them an OSM-M number (where M stands for Massachusetts) to signify new contributions from you guys. Also, I noticed that your students are numbering each experiment. Would it be possible to have a number corresponding to a molecule followed by a number corresponding to the version of a reaction? So, BS15-1 and BS15-2 would correspond to sequential attempts at the synthesis of the same molecule? Not a problem for now but this means it is easier to keep track of compounds.

In terms of sharing data and keeping up to date I am reluctant to return to ELN pages that collate links as the upkeep is just too great. I still don't know the best solution to this problem as we end up spending too much time manually entering data that we'd like to automate when possible.

One intermediary solution is to use a Google Sheet that could also be used to keep an eye on an experimental write-up suitable for publication: https://docs.google.com/spreadsheets/d/1D6i_IfTQnpXdWREYATEEX4AKOd2ov_-hGeKaRCJLruk/edit?usp=sharing

The alternative is to set up GH pages with all links added by chemists as they attempt a reaction but I know that it is hard to remain diligent with administrative duties when busy in the lab.

We can add links to lab books and also use the key (green = done, amber = something missing, red = not collected, grey = not required) and also share an experimental write-up file. This means that we won't end up duplicating unnecessary data collection such as HRMS or 3D NMR experiments.

What do you think?

mattodd commented 9 years ago

Excellent points. Happy to go with whatever works best. A spreadsheet is likely the way to go. Question: could we not just add these to the "end" (extreme right hand side) of the existing Master Sheet? All the strings are already in there... As well as the chemist's codes/synonyms. The spreadsheet becomes large, but one can always split the screen. @lpatiny already, or will soon, have the ability to take raw NMR data for compounds and display that in Cheminfo. If we, in future, linked to raw data files for compounds (e.g. in your grid, Alice, where the colour shows that the file is there, but the text in the cell locates the file) then the NMR spectra can be browsed online too...

Chase - your middle letter for the OSM codes (for things we've not made before in the project) would depend on which city you're in. Boston, Manchester or Worcester.

On 11 November 2015 at 14:54, alintheopen notifications@github.com wrote:

Hi @mattodd https://github.com/mattodd and @MedChemProf https://github.com/MedChemProf

The compounds made to have OSM-Snumbers. @MedChemProf https://github.com/MedChemProf if your team make anything that hasn't already been made by the project then you should give them an OSM-M number (if M stands for Massachusetts) to signify new contributions from you guys. Also, I noticed that your students are numbering each experiment. Would it be possible to have a number corresponding to a molecule followed by a number corresponding to a repeat of a reaction?

So BS15-1 and BS15-2 would correspond to sequential attempts at the synthesis of the same molecule? Not a problem for now but this means it is easier to keep track of compounds.

In terms of sharing data and keeping up to date I am reluctant to return to ELN pages that collate links as the upkeep is just too much. I still don't know the best solution to this problem as we end up spending too much time manually entering data that we'd like to automate when possible.

One intermediary solution is to use a Google Sheet that could also be used to keep an eye on an experimental write-up suitable for publication: https://docs.google.com/spreadsheets/d/1D6i_IfTQnpXdWREYATEEX4AKOd2ov_-hGeKaRCJLruk/edit?usp=sharing

The alternative is to set up GH pages with all links added by chemists as they attempt a reaction but I know that it is hard to remain diligent with administrative duties when busy in the lab.

We can add links to lab books and also use the key (green = done, amber = something missing, red = not collected, grey = not required) and also share an experimental write-up file. This means that we won't end up duplicating unnecessary data collection such as HRMS or 3D NMR experiments.

What do you think?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-155654591 .

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

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.

alintheopen commented 9 years ago

I'd definitely like to keep the SS separate, much easier to manage. Will also hyperlink straight from chemist code to the ELN entry to save a column.

MedChemProf commented 9 years ago

@mattodd and @alintheopen - I have made a number of changes to our notebook pages to be better align with the OSM tracking needs. Please have a look and let me know where I might have made any mistakes or not followed your intent. With only a few pages generated so far, making any needed modifications to our notebooks now will be much easier than later. I selected "W" as our middle letter with respect to Matt's comment on the city name. We are proud to be Worcester since many people think that Boston is the only city in Massachusetts.

With regards to numbering the intermediates, I need a little help identifying were I can search for a particular number that would eventually end up in your synthesis tracking spreadsheet. As an example, the following link (http://malaria.ourexperiment.org/triazolopyrazine_se/9648/Synthesis_of_5chloro34chlorophenyl124triazolo43apyrazine_JU_81.html) in the LabTrove notebook details the synthesis of the same intermediate that corresponds to my notebook (CCS-2-1) and which is given an OSM number in your spreadsheet (https://docs.google.com/spreadsheets/d/1D6i_IfTQnpXdWREYATEEX4AKOd2ov_-hGeKaRCJLruk/edit?pli=1#gid=0) of OSM-M-X. Where in the LabTrove notebook would I find the number that corresponds to the 'X'?

Thank you and please let me know if you need any clarifications to my questions.

lpatiny commented 9 years ago

In your notebook page it would really be great if you already save today the spectra as Jcamp-dx. From bruker spectrometer the instruction is "tojdx". Please save after FT and phase correciton. We will be able to display them on-line. For IR it is a common exportation format. For Mass it is less obvious but we will come with a solution soon. Saving the scheme as a RXN file or chemdraw file is always interesting as well.

drc007 commented 9 years ago

I’d fully support this, JCAMP is now a very widely used format and there are a number of open-source tools that can be used to display the spectra.

On 12 Nov 2015, at 06:36, lpatiny notifications@github.com wrote:

In your notebook page it would really be great if you already save today the spectra as Jcamp-dx. From bruker spectrometer the instruction is "tojdx". Please save after FT and phase correciton. We will be able to display them on-line. For IR it is a common exportation format. For Mass it is less obvious but we will come with a solution soon.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-156014593.

lpatiny commented 9 years ago

Actually there are our tools that allows to display 1D and 2D spectra. You may test them using google chrome : http://www.nmrdb.org/hmbc/index.shtml

We will also be able to integrate on-line assignment in a close future (we are currently sending a publication about it)

lpatiny commented 9 years ago

By the way if you are interested in structural analysis you may have a look at the tools I provide to my students (also using google chrome ...) http://www.cheminfo.org/flavor/structuralAnalysis/index.html

MedChemProf commented 9 years ago

I can investigate the export of the jcamp files. Our situation is that MCPHS (Worcester) does not own its own NMR. We end up renting time on an instrument at a nearby university. That particular instrument is set-up in a 'Walk-Up' fashion and we only acquire the data which is then emailed out to us in a zipped format. I then process the zipped file using MestreNova Lite. The raw NMR data is included in our notebook in the zipped file. Can the raw zipped NMR data file be used directly? The MestreNova Lite does seem to have the ability to save a jcamp file if the original file is not suitable.

lpatiny commented 9 years ago

We are working in the bruker converter in javascript that would accept directly the zip file but this is not done yet some I can not be sure 100% it will work. I think however jcamp is quite standard and maybe it is just an option for them to add it in the zip. But anyway the zip is better than nothing !

MedChemProf commented 9 years ago

Not a problem. I will look into trying to get this worked out on our end.

mattodd commented 9 years ago

Ah JCAMP - I blogged about that a few years ago when we were just getting started. It was glitchy. Are things better? The only problem as I see it is if we're asking people to do a certain thing, we have to be sure that we are all happy to do it. At the moment we are (meant to be) saving PDFs of NMR spectra and the raw data file into an ELN entry. Adding JCAMP to that is one more step, but when one is busy remembering to do this each time can be a drag, and people start not bothering. So my question is: how important is this? If we save in a proprietary format, is it still the case that there are no converters?

Obviously if there were tools to visualise NMR data based on JCAMP that could be plugged into, for example, @lpatiny 's system, then there is an active advantage (to the researcher) in uploading the JCAMP file and people might be interested to do so. Less good than if proprietary formats could be read, but still a positive incentive. I'm thinking of the case where a JCAMP file has a URL (as it would when e.g. posted to Labtrove) and if that URL is part of a synthesis mastersheet, then the data could be visualized automatically.

@MedChemProf - if there is a compound with OSM-M-X in the sheet, perhaps @alintheopen put it there in anticipation? Not sure we have any "M" compounds yet? The answer to the question is that: before assigning a number, we'd need to check in the Master sheet that the molecule has not been made already. We ought to use the Master sheet as the ultimate source for this, since it's more easily searchable than disparate ELNs. This could result in someone making a molecule, or attempting to make a molecule, and for someone else, later, giving it an OSM number when it hits the sheet. I think we'll have to live with that. I'm fairly relaxed on the question of whether we give OSM codes to molecules we don't evaluate biologically, though opinions differ on this. When writing up the Series 1 paper is was pretty convenient for every intermediate also to have an OSM number, whether or not that compound had been tested for activity. So in short I think perhaps the number goes to the person who has made it and is first to enter it? Another incentive!

lpatiny commented 9 years ago

At my point of view proprietary format and opensource are not really compatible words. Same is true for the perennity of the information. So at least the jcamp format should be there. In mass spectroscopy the same problem appears where some proprietary format can only be read by proprietary software. The goal is really that anybody have access to the information so all the format used should be described and readable.

drc007 commented 9 years ago

JCAMP is a plain text file format so that even way down the line someone could read the file with just a text editor, and if need be create a viewer. I'd fully support it's inclusion.

mattodd commented 9 years ago

OK, it'd be good if someone wanted to post a JCAMP to the ELN so that we could play with that - to see if it's easily readable (should be) e.g. by Luc' system.

I'm 100% for open standards. I know that we'll need to post the proprietary formats, since that's what we use internally, meaning that posting JCAMP will involve another step, for every experiment. If there was a converter that took in proprietary and spat out JCAMP that'd make everyone happier.

On 15 November 2015 at 03:45, Chris Swain notifications@github.com wrote:

JCAMP is a plain text file format so that even way down the line someone could read the file with just a text editor, and if need be create a viewer. I'd fully support it's inclusion.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-156718675 .

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

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.

MedChemProf commented 9 years ago

I will be heading over to WPI this Thursday to catch up on a number of NMR and LCMS samples. The NMR facility there has agreed to automate the export of both the zipped data file and a jcamp file from our samples. I will add both to our ELN once acquired for anyone to have a look at. Hoping this should work.

lpatiny commented 9 years ago

If you have a NMR jcamp file you can drag / drop it on the page:

http://www.cheminfo.org/Spectra/NMR/Predictions/1H_Prediction/index.html?viewURL=http%3A%2F%2Fcouch.cheminfo.org%2Fcheminfo%2Feea0ba081ea2cc99da5c1aed2f29a0a8%2Fview.json%3Frev%3D40-40f7caafd596062acba02e6e0570d3ea

Please note that this jcamp file have to be AFTER FT !

This page allows to predict the spectra but also to superimpose the experimental spectrum

lpatiny commented 9 years ago

Concerning conversion program we are writing some of them but I would prefer if the spectro could directly export the data correctly. Clearly for IR and UV jcamp is enough and the original file does not have to be kept. For NMR because we save the file after fourier transform it is better to keep somewhere the original file.

mattodd commented 9 years ago

OK, so we could have people upload the raw data file (whatever source), then FT the data and generate a picture for humans, then upload the JCAMP of that FT'd dataset. I think this is where we were before, and that extra step of remembering to generate the JCAMP was, for people taking NMR spectra every day, sufficiently annoying that we saw compliance creep down over time. If there was a nice positive reason to supply the JCAMP, like the kind of visualisation you're describing Luc, then perhaps we can be more effective in promoting JCAMP. Let's go with some trial complete entries and see what comes of it.

On 16 November 2015 at 20:47, lpatiny notifications@github.com wrote:

Concerning conversion program we are writing some of them but I would prefer if the spectro could directly export the data correctly. Clearly for IR and UV jcamp is enough and the original file does not have to be kept. For NMR because we save the file after fourier transform it is better to keep somewhere the original file.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-156972396 .

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

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 commented 9 years ago

Bruker spectrometer does a good job FT automatically and convert to jcamp. It should therefore not be a problem to have an automatic process. We could make in a ELN an automatic workflow that store the spectrum in the ELN. It is what we have internally at EPFL.

MedChemProf commented 9 years ago

@mattodd and @alintheopen During the last Google Hangout meeting, there was mention that you were looking for Mentors for some of the students that were working on the OSM chemistry. I was wondering how to find out more information on this particular subject. I sent out a number of emails to various colleagues and two are interested in mentoring (one is a Medicinal Chemist in Discovery Chemistry at Teva Pharmaceuticals and the other is a Director of DMPK at Merck.) Please let me know what the next steps are to be taken. While they both were looking forward to mentoring, the common question from both was what was the expectation for time commitment.

mattodd commented 9 years ago

I'd say this is very much up to you, Chase. My ballpark was that 5 students working full-time would benefit from one experienced chemist for half an hour a week, or something along those lines, but perhaps this could be reviewed at the end of a project. A requirement would be that comments should be in the public domain - this both helps with allowing others to contribute too but crucially helps to make sure that this level of input is clearly acknowledged. The comments should not be anonymous, and it helps if mentors are therefore carrying their employer names with them - this may need some clearance internally, but hopefully this is the kind of outreach work that employers are actively encouraging. The time needed would depend a little on how well the research record is kept - a beautifully maintained lab notebook is easier to analyse than one that is badly maintained. Clearly if students wanted advice on something specific, then it would help if those questions could be specifically posed, but there is value in just having a mentor oversee research that is going on in a fairly unstructured way, commenting on whatever comes to light - this obviously mimics quite well any regular interaction between student and mentor in a science project. There also needs to be a simple place for any feedback to be provided - an online location everyone is content to use. Here (Github) is good, or within the lab notebooks themselves, perhaps in a separate "review" folder in Labarchives to which the mentor has write access - anything that keeps to a minimum onerous logins. The people you mention sound excellent. We can obviously acknowledge any formal inputs on the OSM homepage if that was OK with mentors.

On 17 November 2015 at 23:54, Chase Smith notifications@github.com wrote:

@mattodd https://github.com/mattodd and @alintheopen https://github.com/alintheopen During the last Google Hangout meeting, there was mention that you were looking for Mentors for some of the students that were working on the OSM chemistry. I was wondering how to find out more information on this particular subject. I sent out a number of emails to various colleagues and two are interested in mentoring (one is a Medicinal Chemist in Discovery Chemistry at Teva Pharmaceuticals and the other is a Director of DMPK at Merck.) Please let me know what the next steps are to be taken. While they both were looking forward to mentoring, the common question from both was what was the expectation for time commitment.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-157363631 .

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

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.

MedChemProf commented 9 years ago

@alintheopen It looks like the azide substitution works well as long as the reaction is kept at room temperature and not heated ( https://mynotebook.labarchives.com/share/MCPHS%2520MedChem/MzgwLjl8MzY3Ny8yOTMvVHJlZU5vZGUvMzU2NzYxNTYxNXw5NjYuOQ== ). I will look at the reduction of the azide to the amine in the near future. Famous last words, but I do not anticipate this being a problem. The plan would then be to scale to provide enough starting material for the students to begin synthesizing the reverse amides, ureas, and we might as well make a few sulfonamides. The student work will unfortunately not begin until January. I was also going to comment in the thread #361, but in the mean time, can a registration number be generated for the azide? Thank you.

azide

 Finally, I have started including the jcamp .dx files for the NMR in our lab notebook. The facility where we obtain the NMR has begun sending me the jcamp .dx file, but I was not able to get it to work on the site that @lpatiny had provided. I think the reason is that the .dx file is generated pre-FT and not post-FT. I will be discussing with the facility if it is possible for them to modify how they are sending me the data. For the time being, I generated the correct .dx file to be stored in the ELN from the third party MestreNova software. While this was not too troublesome, I agree with @mattodd that I can see future instances where the chemist forgets to do this.

mattodd commented 9 years ago

Great stuff, Chase. Looking forward to seeing how that reduction goes. That would provide access to a bunch of the compounds in #358. I just invited you to have edit rights on the Master Sheet. Feel free to add in compounds you're making. OSM-W-X, right?

alintheopen commented 9 years ago

Great indeed @MedChemProf. Yes, it is much better if you can create the OSM codes for your molecules, keeps the task more manageable and hopefully prevents any duplication.

I have uploaded JCamp, PNG, PDF and zipped files to the ELN for AEW 261-1 (http://malaria.ourexperiment.org/triazolopyrazine_se/13768/Synthesis_of_R2dimethylamino2phenylethan1ol_AEW_2611.html) Also tried this in @lpatiny's website - dragged JCAMP file to visualise spectra and overlayed with predicted spectra created on same page. Very nice.

Will also link to HRMS and IR (Jcamp) for other compounds. What is the preferred non proprietary file type for HRMS data?

drc007 commented 9 years ago

This looks very nice.

I’m not sure there is a preferred format for HRMS data but I know you can also use JCAMP. There are a variety of formats mentioned here https://en.wikipedia.org/wiki/Mass_spectrometry_data_format https://en.wikipedia.org/wiki/Mass_spectrometry_data_format

Cheers,

Chris

On 24 Nov 2015, at 05:28, alintheopen notifications@github.com wrote:

Great indeed @MedChemProf https://github.com/MedChemProf. Yes, it is much better if you can create the OSM codes for your molecules, keeps the task more manageable and hopefully prevents any duplication.

I have uploaded JCamp, PNG, PDF and zipped files to the ELN for AEW 261-1 (http://malaria.ourexperiment.org/triazolopyrazine_se/13768/Synthesis_of_R2dimethylamino2phenylethan1ol_AEW_2611.html http://malaria.ourexperiment.org/triazolopyrazine_se/13768/Synthesis_of_R2dimethylamino2phenylethan1ol_AEW_2611.html) Also tried this in @lpatiny https://github.com/lpatiny's website - dragged JCAMP file to visualise spectra and overlayed with predicted spectra created on same page. Very nice. https://cloud.githubusercontent.com/assets/2626599/11358587/00cdd772-92c8-11e5-9331-f8bb91998201.png Will also link to HRMS and IR (Jcamp) for other compounds. What is the preferred non proprietary file type for HRMS data?

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-159153259.

lpatiny commented 9 years ago

For HRMS we can load jcamp or tab-delimited files. We really have cool unique tools in the field of mass and I will be happy to present in more details. You may drag drop files to test on the page: http://www.cheminfo.org/Spectra/Mass/MF_from_monoisotopic_mass/index.html?viewURL=http%3A%2F%2Fcouch.cheminfo.org%2Fcheminfo%2F4a06cbbc25197036518fab2ea6ff961d%2Fview.json%3Frev%3D75-0de7fa938fcd11fa917d2ca44c46bb04&dataURL=http%3A%2F%2Fcouch.cheminfo.org%2Fcheminfo%2F4a06cbbc25197036518fab2ea6ff961d%2Fdata.json%3Frev%3D75-0de7fa938fcd11fa917d2ca44c46bb04

lpatiny commented 9 years ago

We plan to support NetCDF that will very likely be a requirement for GC/MS and HPLC/MS but there are no real library available in javascript so we may have to make one.

MedChemProf commented 9 years ago

@alintheopen @mattodd I just updated one of the tracking spreadsheets with the azide and the amine (OSM-W-1 and OSM-W-2 respectively.) The azide reduction appeared to work very well. I want to re-run the C-13, but the proton is very clean and the mass spec correct for the amine product. I will be scaling up closer to the new year in time for the students to use the amine for analoging. One note, it looks like the azide may slowly decompose over time. I had saved some of the material to run a C13, but the sample contained black particulate material upon standing over a four day period. On the book keeping, please let me know if my update to the tracking sheet follows your protocols correctly. If not, please let me know what to change/fix and I will do so. Thanks.

mattodd commented 9 years ago

Looks good to me @medchemprof. If you can check whether there's a pubchem ID, or whether there are any other relevant IDs (i.e. whether the compound is already known by another name) and install those IDs, that wraps it up. OSM-W-2 is series 4, too, right?

On 25 November 2015 at 03:12, Chase Smith notifications@github.com wrote:

@alintheopen https://github.com/alintheopen @mattodd https://github.com/mattodd I just updated one of the tracking spreadsheets with the azide and the amine (OSM-W-1 and OSM-W-2 respectively.) The azide reduction appeared to work very well. I want to re-run the C-13, but the proton is very clean and the mass spec correct for the amine product. I will be scaling up closer to the new year in time for the students to use the amine for analoging. One note, it looks like the azide may slowly decompose over time. I had saved some of the material to run a C13, but the sample contained black particulate material upon standing over a four day period. On the book keeping, please let me know if my update to the tracking sheet follows your protocols correctly. If not, please let me know what to change/fix and I will do so. Thanks.

— Reply to this email directly or view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/352#issuecomment-159317724 .

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

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.

MedChemProf commented 8 years ago

A few of the students presented posters internally here at MCPHS on their current progress in the lab. kenneth_kimberly_mcphs jessie_mcphs

alintheopen commented 8 years ago

Awesome work guys :)

OpenSourceMalaria / OSM_To_Do_List

Massachusetts College of Pharmacy and Health Sciences Join OSM #352