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What's Needed for a Test of Luc Patiny's New System? #372
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should we discuss next steps for this as part of next open science prize On Tue, Feb 2, 2016 at 1:14 PM, Mat Todd notifications@github.com wrote:
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Yes, good idea. On 15 February 2016 at 11:33, alintheopen notifications@github.com wrote:
MATTHEW TODD | Associate Professor THE UNIVERSITY OF SYDNEY CRICOS 00026A |
I was struck by the idea of having pictures next to the notebook in the video, I know it might sound trivial but could we really have a place to store a photo of the notebook owner in the ELN? |
Good idea and I think probably easy to implement? On 29 February 2016 at 00:26, Chris Swain notifications@github.com wrote:
MATTHEW TODD | Associate Professor THE UNIVERSITY OF SYDNEY CRICOS 00026A |
FYI http://www-rinchi.ch.cam.ac.uk/website2015/ The aim of the RInChI project, in the same vein as InChI, is to create a unique data string to describe a reaction. |
Just FYI when thinking about a web-based system. http://www.cambridgemedchemconsulting.com/news/index_files/f0da025f6c2148999e7b530dc89b4c1b-206.html |
Seems strange that Safari range from 9 to 62%. Safari is only working on OsX and iPhone and if we check wikimedia statistics (https://stats.wikimedia.org/wikimedia/squids/SquidReportClients.htm) safari is less than 5%. |
Right, so Luc's new ELN is right to focus on Chrome as the starting point, On 8 March 2016 at 19:21, Chris Swain notifications@github.com wrote:
MATTHEW TODD | Associate Professor THE UNIVERSITY OF SYDNEY CRICOS 00026A |
I guess this is the profile of those involved in drug discovery not the general public. If you walk around a bioinformatics lab it will be nearly all Mac, so for some software vendors it is not surprising that their users are a high proportion of Mac users. Similarly in Computational chemistry, used to be dominated by silicon graphics etc. now Mac and Linux
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@mattodd I just received the below email: |
Too bad! It would have been interesting to receive feedback - it's a great On 23 March 2016 at 22:15, Chase Smith notifications@github.com wrote:
MATTHEW TODD | Associate Professor THE UNIVERSITY OF SYDNEY CRICOS 00026A |
:( can we surface the whiole thing on a blog and/or figshare ? |
@lpatiny @mattodd I just wanted to surface the ELN again focusing on the issue of displaying NMR data on the website. At the moment, when our research group runs an NMR sample, the instrument sends us a pdf overview, a zipped data file as well as a jcamp.dx file. All of these files get placed in our ELN. Furthermore, we process the jcamp file to produce expansions using a commercially available software package called MestreNova. All works well. |
Please could you upload or send me one of the jcamp files ? |
@lpatiny GitHub would not let me paste in the jcamp file, but here is a link to one of mine: https://mynotebook.labarchives.com/attachments/OTA0MS41fDM2NzcvNjk1NS9FbnRyeVBhcnQvMTY5OTk4NjYzfDIyOTUxLjU=/1/original?sf324=343 Here is also the link to the same spectra as the zipped data file directly from the instrument: https://mynotebook.labarchives.com/attachments/OTA0NC4xfDM2NzcvNjk1Ny9FbnRyeVBhcnQvMzE3ODgzMDU0fDIyOTU4LjE=/1/original?sf324=343 Please let me know if the links do not work for you. Thanks for looking into this. |
Indeed this jcamp contains the FID as well as the spectrum after Fourier transform. We currently don't deal with this kind of file but we should be able to add this feature. |
@lpatiny The problem is that we do not own the machine nor actually process or export the data ourselves on the machine. We borrow time on another universities instrument and they cut us a break on costs. While they are usually very helpful, I am not sure just how much we can ask them to change their normal protocols on a very busy machine. |
This will be solved by a new module that we are currently creating. |
@lpatiny Thank you for your help on this. |
@lpatiny @mattodd @MedChemProf Worth a read https://peerj.com/preprints/2325/ |
@drc007 @MedChemProf @lpatiny |
@mattodd I finally got a chance to read through the preprint and to be honest, nothing really surprised me. More to the point, it underscores that the problems that we have been encountering in the OSM are general in nature and are in need of a solution. My view of the marketed (free and paid) ELNs is that they each solve only parts of the problem and are not truly comprehensive. (The complete packages of ELN, LIMS, etc. tend only to be available at companies and institutions that have a dedicated IT/Programming staff to support those complex systems.) With all that being said, research is becoming more and more collaborative across disciplines and geography, making ELNs an inevitability. Early collaborative drug discovery and research would be greatly benefited by an open ELN with something like SCINDR monitoring for overlap and duplication. I think as long as we are careful to very specifically define the boundaries for the OSM Open ELN/SCINDR, we will eventually find funding. |
Hi @lpatiny . What we'd love to do is this:
So: first step. After discussions here it looks like the simplest place to put our example data, for one chemical reaction, is on a public Dropbox folder. Is that OK?
If no, where should we instead put the data?
If yes, can you tell us (bench chemists) how you want the data arranged - i.e. names of folders and filenames, and types of data.
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