stolarczyk/metabolite

Shiny app for visualization of the toy GENREs

metabolite's Issues

transcriptomics experiment visualization

The graph does not change after the expression of the genes changes

Color code for localization

Use different color for nodes that represent metabolites in different compartments

Code annotation

Annotate the server.R file (comments, sections)

KO reset simplification

Do not use the media changing Python script. Use the regular visualization instead

emphasize main metabolites

Make main metabolites names bigger

Fix error

Warning: Error in which: object 'ori_objective' not found 73: which 72: observeEventHandler [/Users/mstolarczyk/Uczelnia/UVA/shinyapp/server.R#1953] 1: runApp

Fix the error above when running the experiments

Popovers after clicking on "?"

Gene knockout as opposed to reaction knockout

Change the reaction knockouts to gene knockouts. Make changes to the list - should be similar to expression experiment one

dashed lines legend

Add dashed lines mean zero flux in each visNetwork graph

Technical popovers

Add technical popovers so that they are not overwhelming the user

App/model name

What's the app name?

Help

Work on help tab contents and get rid of the overwhelming popovers

NoName reactions Ecoli

Get rid of the NoName reactions in Ecoli (KO tab?)

Network visibility

Make the network visible at all times. For example when launching the tab for the first time

Work on installation instructions

Have link for each OS.

Add: Open the docker application to ensure it downloaded correctly. (On Macs, there will be a green circle)

Open the command window (give instructions for each operating system).

Add: Copy and paste the text to download the tool using Docker.
Then add a lay-person description of what Docker does - something like 'This contains all the necessary requirements to run our tool.'

3. See if the image has been downloaded. Just use the command:

docker images

Add a lay person description of this step.

and copy the IMAGE ID

Add a screen shot of what people should expect and what they need to copy.

This binds port 8080 of the container to the TCP port 8080 on 127.0.0.1 (local host)

This description only makes sense to a very computer-literate person (I barely understand it). Please add a lay person translation, something like ' Copy and paste this text into your command window. This will allow you to connect to the downloaded tool from your web browser.'

5. Open a browser and paste:

localhost:8080

Again, add a lay person description.

metabolites names clean up

No chemical formulas in the metabolite names

Dockerfile

Invalid Dockerfile: rsbml r package can't be installed. Multiple errors arise

Zero flux visualization

The edges of the graph carrying zero flux should be gray or dashed lines

Visualization

Filter out the exchange and transport reactions when visualizing the ecoli model

Objective rxn color coding

The objective reaction should be color coded differently.

Legend changes

change the key on the right to say 'cytosolic metabolite' and 'mitochondrial metabolite' instead of 'metabolite cytosol' and 'metabolite mitochondria'.

Disappearing popovers

Make the popovers disappear after the tab is changes or after some set period of time

FVA?

Implement Flux Variability Analysis.

How to present the results?

Sections titles

Title the sections of the sidebar
Bigger fond headings

• Analysis setup
• Results

New help tab

Make and additional "help" tab instead of technical popovers with the documentation and biological meaning

Cosmetic changes to the UI

• Home tab instead of Visualize tab
• Simulate expression changes tab (?) instead of integrate transcriptomic data tab
• Looser spacing in the Home tab
• Print the current objective function name when displaying the objective value
• Define stoichiometry somewhere
• Communicate searchability of results table

Tabs visibility

Make the tabs visible at all times

headers layout

work on visualize and change media tabs headers layout, vertical spaces too large

RBC model

Change the the ecoli core metabolism model to other small network (maybe the RBC). No lipid turnover and export reactions, or just one compartment possible?

New layout

Implement new layout to:

• - media changing visualization

• - gene expression simulation visualization

• - reaction KO visualization

The most challenging (rxn KO) can be done as follows:

1. Flux calculation and model manipulation as it is (Python)
2. Use KOed reaction ID to modify the modified model to visualize

Changing the objective

Make the objective function changing possible. Possibly as a list of reaction that the user can choose from.

Then within CobraPy:
model.objective="rxn_name"