modelseed / modelseed-ui Goto Github PK

and check existing token against url login= param (for patric).

In our "Run FBA" options we have one option that is "Find Min Media", this is actually a pretty cool functionality and we know its work in the backend (at least it was working in the cmd line last time I used it with Chris). But this functionality would require a specific output tab that is non-existent.

I suggest an additional tab to be add to the "FBA viewer" with the output from Min Media, when a user selects that option.

I don't know if this would be a priority or not, but for the website release if we don't plan to have that specific output view tab, we should remove that option from "Run FBA" until that's implemented.

See ModelSEED/ModelSEEDDatabase#27.

undesirable. Should only close when clicking outside. reported by @jplfaria

A user should be able to see the list of reactions for a gap fill solution.
This becomes even more important once the functionality to integrate and remove gap fills solutions is available.

Driven by plants work.

Here are some issues I noticed when doing searches in the microbe genomes:

• If I paste the search term 'Yersinia pseudotuberculosis EP2/+' into the search area, the search seems to go into a never ending loop. If I remove '/+' it finds it fine.
• Mike may have mentioned this already, but sometimes the search gives results that don't match the search. For instance, if you type Yersinia pseudotuberculosis, you will get the results for this organism, but you will also get hits on Yersinia pestis and similis.

as reported by @jplfaria.

reported by @janakagithub

reported by @jplfaria

Should use angular material for this.

I was showing the new website to a couple of people at COBRA and by looking at the biochemistry page I was asked if we had KEGG IDs and E.C. numbers as those were available in old ModelSEED.

@cshenry are we planning to add these back?

per @janakagithub

User tried to run reconstruction with custom media (built from UI) and gapfilling failed with:

Use of uninitialized value $Item in concatenation (.) or string at /disks/p3c/deployment/lib/Bio/KBase/ObjectAPI/utilities.pm line 332.
Type retrieved (string) does not match specified type (media)! at /disks/p3c/deployment/lib/Bio/KBase/ObjectAPI/utilities.pm line 183.
Bio::KBase::ObjectAPI::utilities::error("Type retrieved (string) does not match specified type (media)!") called at /disks/p3c/deployment/lib/Bio/ModelSEED/ProbModelSEED/ProbModelSEEDHelper.pm line 196
Bio::ModelSEED::ProbModelSEED::ProbModelSEEDHelper::error(Bio::ModelSEED::ProbModelSEED::ProbModelSEEDHelper=HASH(0x3335140), "Type retrieved (string) does not match specified type (media)!") called at /disks/p3c/deployment/lib/Bio/ModelSEED/ProbModelSEED/ProbModelSEEDHelper.pm line 41
...

I suggest this change because I believe its more intuitive when one wants to open an FBA solution for the link to the element that open a solution to be in the first column.
This is even more important when we give the user the option to name their FBA solutions.

Here are some suggestions for the Model page.

1. Add a Summary tab that includes the data returned in a ModelStats structure.
2. Remove the ID column from the Reactions and Compounds tabs. Change the Name column to a link that shows the popup window with the details.
3. On the Reactions tab, make the compounds shown in the equation a link that shows the popup window with the details.
4. On the Biomass tab, change the display to a list of the biomass reactions. Then allow the reaction to be expanded to show the compounds. The compounds should just show the name, coefficient, and compartment with the name a link to the popup window with the details. Separate the compounds i5.nto reactants and products (most people aren't going to know what a negative coefficient means).
5. On the Gapfilling tab, add a way to show the reactions added or changed by the gap fill.

• 1) remove all advanced options in reconstruct/fba/gapfill (for now)
• 2) enhance my models page with status* [stalled]
• 3) enhance notifications with completion status
• 4) fix the comparison page :(
• 5) remove fba/gapfill counts (for now)
• 6) add 'forgot password?' link to RAST/PATRIC
• 7) add help text on how to annotate gnomes via RAST/PATRIC
• 8) spruce up 'my models' as time allows
• 9) point model view gene links to RAST
• 10) move user to 'my media' after copying media
• 11) log out of other tabs/windows on logout.

'*' involves significant time over other items.
Commit messages will follow below. Deployed items are checked above.

In the model viewer, if you click on the link for a reaction in the Reactions tab, a new tab for the reaction is added but it hangs in "loading". Maybe the lookup needs to remove the compartment suffix?

This would be a good way of driving the use of a "Documentation" repo.

Hi

I wonder if the ModelSEED API could return the ModelSEED database version.
Regards

@janakagithub has volunteered by providing the data needed for this.

Push toward using ES6 for modules and other features.

On the Biochemistry tab, if I go to the "Public Media" section and click on a media, a page is displayed that shows the compounds in the media. When I click the back button in the browser, the "Reactions" section is displayed instead of the "Public Media" section. That's frustrating if you searched for media and have to repeat the search after looking at the media that you found.

I've been meaning to do this. Should show “unknown” or “unspecified” for deltaG and deltaGErr's that are “1000000".

Reported by @chian.

It seems the my-media reconstruct dropdown doesn't dropdown after the first time switching to it. Reported by @chian

On the "Run FBA” would be good to have an option to name the FBA run. After 10+ FBAs gets very difficult to track what was done in each run. I suggest either that or renaming of the IDs on the list of FBAs.

I think ideally we would actually want both ways suggested above, but at this point whatever would be easier to implement should be the way to go.

The number of reactions and compounds is inconsistent between the summary of the model page (see screenshot) and the tabs in the model viewer. I think the values on the summary page are the ones that are incorrect (reaction and compound numbers are reversed).

This option is currently listed in Run FBA as "Simulate Gene Knockout?", it should be something like "Simulate All Single Gene Knockouts".
This would also require a specific output, I suggest to add a "Genes" tab to the FBA results, similar to the "Genes" tab we already have in the Model tab. On that tab the result of the KO would be shown for each gene.

Like I mentioned in a previous issue, if we are not planning to support this issue at release, we should remove it from the options.

This includes links for new tabs on reactions, compounds, compartments. Also external links for genes and org name.

Currently we don't have option to do gene KOs in FBA (only reaction KOs).
The implementation of reactions KOs with the search looks pretty neat, an exact same field for gene KOs would be ideal.

Hi,

I am trying to create new media compositions that include dipeptides and tripeptides but can't find any of these compounds within Model Seed to add to the media.

Would you be able to help us with this please? Is there a way to add new dipeptides and tripeptides compounds with the corresponding ID, Formula, deltaG, detalGerr and charge for each peptide?

Many thanks

Anna

• Add support for editing model templates
• Add support for mapping model templates to improved KEGG maps