1. Fall 2015 Course
  2. Discussion

Discussion

Robert Belford's picture
Robert Belford | Thu, 09/01/2016 - 15:31
Hi All, After communicating with some of you, I have decided to hide the modules from the public until we actually go public, and so you need to log into this page in order to see the links to the modules, and the content associated with those links. Currently there has been a lot of activity on the "Programmatic Access to Web-Based Chemical Information" module, and please contact me if you have any questions on how to become more involved. Cheers, Bob

Robert Belford's picture
Robert Belford | Fri, 08/26/2016 - 11:17
Hi All, The OLCCFAC list is now subscribed to the Spring 2017 Development site, and comments to this will trigger emails to everyone who was involved with the Fall 2015 OLCC, or has become involved with the Spring 2017 OLCC. I will shortly add potential facilitators who showed interest at the BCCE and lecturers/facilitators whom I interacted with this week at the ACS meeting, but I want to do that with a personal email. Please send me a private email if you were in the 2015 class and wish/need to be updated. I am currently in Menlo Park CA (I was at Google yesterday and will be at the Institute for the Future later today), and then go visit a friend who does not have internet access. So I may be out of touch from Sat-Monday (I fly back to AR on Monday). There are currently 5 links on this site (and more coming), the first two are to the retreat discussions, which you may want to peruse if you did not go (you need to log in to see the files that are attached), and a module that will span the entire course on introducing students to programmatic access to data, and then there are the first 3 of 8 modules that we will be running in the spring. These will not have clear start/stop dates like in a Confchem paper, but overlap with that lecturers collaboratively teaching over several weeks, as the start/stop each week was a problem with the Fall offering (students need more time to figure things out and interact with faculty). A full month (April) will be devoted to projects, and we are looking for mentors. A real lot is going on, and we may have 19 schools on board, at least that many (or more) have shown interest, and I need to get to work before they lose their interest. But a lot has happened, and I will be on task next week. Now, these are collaborative work spaces. You should subscribe to comments on any of the modules you wish to be involved with, and you are welcome to lurk. Everyone will get comments to this module, and if you were involved with the Fall 2015 class and do not wish to be involved with the 2017, you need to unsubscribe to the OLCCFAC list. I can do that if you have problems, just email me in private. So please understand, a comment to this module goes out to the entire faculty involved with this course, lecturers, facilitators and lurkers who are interested in the project or whom may wish to be mentors and work directly with students on student projects. I think we learned a lot last Fall, and lets make this Spring a real success! Cheers, Bob

Herman Bergwerf | Sat, 08/13/2016 - 08:28
Just an interesting link I came across: <a href="https://github.com/KevinLawson/excel-cdk">https://github.com/KevinLawson/excel-cdk</a>

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

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. 

 

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>

Robert Belford's picture
Robert Belford | Wed, 02/24/2016 - 14:43
Here are some interesting stuff, <a href="http://chem-bla-ics.blogspot.com/2016/01/adding-chemical-compound-to-wikidata.html">http://chem-bla-ics.blogspot.com/2016/01/adding-chemical-compound-to-wikidata.html</a> This lead me to Hay's tools: <a href="http://tools.wmflabs.org/hay/">http://tools.wmflabs.org/hay/</a> of which the tool directory may be of interest <a href="http://tools.wmflabs.org/hay/directory/">http://tools.wmflabs.org/hay/directory/</a> <a href="https://www.ebi.ac.uk/efo/webulous/">https://www.ebi.ac.uk/efo/webulous/</a>

Andrew Lang's picture
Andrew Lang | Tue, 02/23/2016 - 11:41
Hi Perry, I can help you. Please contact me at alang<at>oru.edu

Perry Sharma (not verified) | Tue, 02/23/2016 - 11:04
Hello, Dr. Lang Thank you so much for providing the scripts for the solubility calculations. So far I have only been able to access one of the scripts and its the one that converts mole fraction to molarity. What I am doing is I am translating the PHP script and then inserting the code into the google sheets code to scrape for variables such as solute density, solute molecular weight, etc. I've had success obtaining the molecular weight from Cactus using Google scripts but I am unable to obtain the densities from Cactus. It that because Cactus does not provide density data? Is there a Chemspider URL API scheme that I can use to obtain density from Chemspider instead? Also, I was wondering if you would like me to replicate the PHP scripts in Javascript and then use them in the Google sheets or would you like me to use the Javascript in the google sheets to directly access the PHP scripts you provided? Lastly, I was wondering if the rest of the calculation scripts can be accessible? Because so far I have only been able to access one. Thank You Perry Sharma

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.