Feature/add simid

[seliv55]

SIMID is a new tool, written in R, designed for primary analysis of raw data recorded for a great variety of metabolites by mass spectrometers in SIM (selected ion monitoring) mode and saved in netCDF files. It evaluates the peaks of mass isotopomer distribution (MID) of metabolites of interest using the provided netCDF files and a simple text file containing a short description of the characteristics allowing to localize in the records the metabolites of interest.

[pcm32]

Thanks Vitaly! Could you please confirm that:

• It works fine with minikube
• That the output of simid can be succesfully used in Galaxy to feed in midcor (or the step of the workflow that would go after simid?).

Thanks!

[pcm32]

Can I suggest as well that you add a workflow file to workflows/ with an appropiate name, that shows the use of simid with the other tools? Thanks!

[seliv55]

Thanks Pablo for reviewing it!

Yes, I checked, it works fine with minikube.

Simid writes its output in the same format as Ramid or cdf2mid, so It should be compatible with midcor, but I have to check it.

I will do it.

Vitaly

On 04/04/2018 02:11 PM, Pablo Moreno wrote:

Thanks Vitaly! Could you please confirm that:

• It works fine with minikube
• That the output of simid can be succesfully used in Galaxy to feed in midcor (or the step of the workflow that would go after simid?).

Thanks!

[seliv55]

OK, good, I will do it. Thanks for this suggestion. Vitaly

On 04/04/2018 02:13 PM, Pablo Moreno wrote:

Can I suggest as well that you add a workflow file to workflows/ with an appropiate name, that shows the use of simid with the other tools? Thanks!

[pcm32]

Hi @seliv55! Any chance of adding the workflow using simid to this PR? Thanks!

[seliv55]

Hi @pcm32! Thanks for your concern and help! There is no problem to connect simid with midcor; they are connected. There are two problems in connection with Isodyn. First, since the CDF files analyzed with simid contain many metabolites, some of them are not recorded well by the MS machine. We discussed this with our experimental team, and they say that it makes no sense to pass all the automatically corrected data to simulation by Isodyn. The corrected data should be manually selected before the simulation step. The output of midcor should be made convenient to facilitate the manual selection and corresponding editing, whereas the currently used format is very inconvenient. So, I made the output of midcor convenient for manual checking. The input for Isodyn I adjusted correspondingly. So, this is done, but in this way, the workflow is restricted by the two first steps: simid-midcor. Simulation normally takes much more attention than the first steps of data preparation and we think that better not to connect it in the automatic workflow, but keep Isodyn as a separate tool. Are you agree? Nevertheless Isodyn accepts the output of midcor and ane selection of data from it without additional editing. Second, the data, which I have now as an example for simid, contain more than one GCMS fragment of each metabolite. Isodyn was designed for the simulation of mass isotopomers in only one fragment of each metabolite. Now I am changing the design of Isodyn, so that to make it able to simulate the mass isotopomers in various fragments. Hope to finish this soon.

[sneumann]

Do we need this to be merged for tomorrows demo ? Can the demo show the two parts 1) simid-midcor, and after manual curation Isodyn ? Yours, Steffen

[djcomlab]

Any updates expected for this?

[seliv55]

Sorry, David.

Finally we used the improvements developed as "simid" to upgrade "Ramid" and "cdf2mid". Simid itself has some additional useful functionality, but we would like to improve its communication with the existing workflow and implement it in PhenoMeNal later, during the period of maintenace.

On 06/22/2018 05:25 PM, David Johnson wrote:

Any updates expected for this?

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