OLCC Project 2: Integration of a Spectral Viewer in an Open Source ELN

Abstract: Open Source Electronic Laboratory Notebooks (ELNs) have been around for several years and many of these are now specialized for a particular branch of science. Chemistry based ELNs are often challenged with an additional need to store various types of data files and the associated metadata specific to a type of lab instrument. These formats often contain spectral information, resulting in the further need to have graphical based viewing within the ELN. Traditionally, this would be performed by uploading the spectrum in the form of exported images and screenshots which is only a static graphical representation of the raw data. The purpose of this project is to embed a browser based spectral viewer into the ELN that will read the raw data values and output a form that allows for user interaction while preserving the original data.
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OLCC s12's picture
OLCC s12 | Tue, 02/16/2016 - 23:11

Several attempts were made to bring up the JavaScript libraries within the ELN today. The HTML shows up as needed in the source, but the visual display is still not showing up. Tomorrow I will determine where the link to a reference is broken and apply a fix so charts display properly. This will get the initial integration where it needs to be to start working with handling spectral data.

OLCC s12's picture
OLCC s12 | Thu, 02/18/2016 - 17:29

Last Night, I was able to make some progress on the integration.  Some of the updates include moving the repository into the ElabFTW system. Then the JavaScript libraries were moved into the JS folder alongside other JS files being used for ChemDoodle. The source page for the visual interaction portion of the Specktral viewer was placed into an iFrame on the viewXP.php page of the system. CSS adjustments are still needed if the spectral viewer is to work with mobile device scaling or atleast anything other than a full desktop viewing mode. The database handling is still needed to make the spectral viewer grab uploaded files. This will require tracing all of the database entries created when a file is uploaded and setting the SpeckTackle spectral viewer data loading to grab the link to the data. 


To answer Dr. Bauer about the file type being recognized when uploaded, the answer is yes it will recognize the file type being uploaded. I just need to set the spectral viewer to look where the files are being uploaded into the system by the lab notebook so that it has both pieces available. 

Robert Belford's picture
Robert Belford | Wed, 02/24/2016 - 14:43
Here are some interesting links <a href="http://chem-bla-ics.blogspot.com/2016/01/open-spectral-database.html">http://chem-bla-ics.blogspot.com/2016/01/open-spectral-database.html</a> <a href="http://cdsouthan.blogspot.se/2015/08/joining-chemistry-between-journals-and.html">http://cdsouthan.blogspot.se/2015/08/joining-chemistry-between-journals-and.html</a>

OLCC s12's picture
OLCC s12 | Thu, 02/25/2016 - 23:08

Completed since the last progress log:

  • Fixed SSL certificate issue within elabFTW that was conflicting with the spectral viewer.
  • Routed javascript internally to use localhost relative addresses instead of url based.
  • made several macros to convert the agilent GC-MS spectral file to a json spectral file.
  • Made a new html file to insert into ELN entry page to only show GC-MS spectra for GC-MS notebook entry. 
  • Routed the spectral viewer to read the uploaded spectral file. 
  • Uploaded lab entry to coorelate with the spectral file.
  • Fixed the scaling problem inside the defined coordinates of the default specktackle chart. 
  • enabled the group labeling.
  • uploaded relevant .mol files for compounds found in the spectra.

At this point the project is to the point that a good presentation can be given on the ability of the ELN to include interactive spectral display for lab entries.

Additional Goals Before Presenting will be to:

  • Convert the html page to php.
    • make links to have spectral reader grab dynamic spectral files that are relevant to each lab notebook. 
    • start with GC-MS because that is the only file I have that works right now and is my own data. 
    • Then add in other spectroscopy methods. 


OLCC s12's picture
OLCC s12 | Sun, 02/28/2016 - 21:05
I have opened up a feature enhancement issue on the github account for the elabFTW development in which I mentioned the current status of the project and the upcoming presentation on the project in San Diego. I have not talked with the main developer since the beginning of the project so I am hoping to hear some last minute input before making the majority of the presentation slides. If any of the mentors and collaborators on this project have any input, please reply to this comment and let me know what you would like to see before the presentation. Also if you would like access to anything, let me know. the screenshot I uploaded with the feature enhancement is linked below. <a href="https://cloud.githubusercontent.com/assets/8638647/13384576/74c2928c-de5c-11e5-8ffa-579e4edd4da2.jpg">https://cloud.githubusercontent.com/assets/8638647/13384576/74c2928c-de5c-11e5-8ffa-579e4edd4da2.jpg</a> Also, here is the updated repository location that I pushed to most recently. I am using the branch Hypernext to sync with the main developers branch. Currently the workflow has an installation for local, development, test, live and a backup server. Although only the development server is running the newest commits. <a href="https://github.com/boots7458/elabftw/tree/hypernext">https://github.com/boots7458/elabftw/tree/hypernext</a> Thanks, Andrew