Recent changes to bugs

#134 Won't load after fresh install

VAISHNAVI M S — Sun, 24 Sep 2023 19:35:17 -0000

I got the same error can you tell me what steps do I need to follow?
Error occurred during initialization of VM
Could not reserve enough space for object heap

wiki not available

Anonymous — Sun, 10 Jul 2022 02:18:41 -0000

Im trying to access optflux wiki and how tos but its getting 404 error.

gene expression

Anonymous — Thu, 10 Mar 2022 14:14:08 -0000

The gene expression data isn't loading when i upload it in simulation>gemini. could you please help to troubleshoot it?

Many models in the optflux model collection are invalid SBML

Matthias König — Thu, 25 Apr 2019 08:31:49 -0000

Hi all,
I checked the models in the SBML optflux model collection available here
https://github.com/biosustain/memote-meta-models
from originally here
https://darwin.di.uminho.pt/models (certificates are expired)

Many of the models have invalid SBML ids
- iCAC490: missing/incorrect reaction ids
- iCyp752: missing/incorrect reaction ids
- iHZ565: metabolite ids, reaction ids, ...
- iCyn731: reaction ids
- iCyc792: reaction ids
- iCyj826: reaction ids
- iRP911: ids
- iCyp752: ids
- iHZ565: ids
- iIB700: ids
- iMA945: ids

Some are incorrect due to other issues
- iMZ1055: problems with local parameter
- iBT721: empty lists
- iJP962: misc errors
- iMH805_775: incorrect notes

Find a list of all problems attached (optflux-errors.json).

Best Matthias

Matthias König, PhD.
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology
https://livermetabolism.com

efm4optflux doesn't finish the calculation

Anonymous — Mon, 08 Apr 2019 20:19:33 -0000

Hello,

I'm trying to calc the EFM of a model, but the opfflux start the calculation and about at 40% of the process it stop and close the EFM window without any message. Any idea of what is happening?
The examples in tutorials were calculated normally.

Thanks.

#134 Won't load after fresh install

Hugo Giesteira — Fri, 09 Jun 2017 09:31:02 -0000

status: accepted --> solved

#134 Won't load after fresh install

Hugo Giesteira — Thu, 08 Jun 2017 18:20:03 -0000

java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

I just redownloaded from that link. It installs to the x86 program files directory. Loaded immediately. Let it update again just to be sure that was the issue (updated simulation and core plugins). Reloaded successfully. I think the issue was somewhere with the java versions, and the replaced files after i swapped java versions. So, taking your suggestion and changing the java version allowed functionality to exist from the standard install files. Thanks.

#134 Won't load after fresh install

Hugo Giesteira — Thu, 08 Jun 2017 17:20:29 -0000

This is very strange. Lets recap just to see if we are skipping something important.

You installed the java 64bit version right? If you do "java -version" it will show something like:
... Java HotSpot(TM) 64-Bit Server VM ...
Make sure it shows 64-Bit Server VM and not Client VM because you can have more than one java installed in your machine but only one associated to the java command;
You also installed OptFlux for windows 64Bit, the one from this link: https://sourceforge.net/projects/optflux/files/LatestRelease/OptFlux-3.3.3-windows-x64-installer.exe/download
After both these steps you execute OptFlux and did run until you perform the plugins update right?
Did you needed to replace both files we talked or the application was executed without the exchange?

If you needed to replaced the files then after the plugin update you must replace them again and it should work.

If after all these steps and the plugins update the application still don't work then we have to say to skip the updates and try to work in the version you installed.
We can't understand the problem you have encountered and unfortunately we cannot help more then this so at least you can execute the latest OptFlux release version so we will hope the next release will fix you problem.

#134 Won't load after fresh install

Hugo Giesteira — Thu, 08 Jun 2017 17:01:34 -0000

The "post awaiting moderation" is killing the speed of this. It loaded after java update, updated plugins, then didnt load. I have since already tried reswapping the two files you provided earlier out with no change.

#134 Won't load after fresh install

Hugo Giesteira — Thu, 08 Jun 2017 16:53:14 -0000

So it worked before the plugins update?

Please replace the main.conf file again. This happens because some plugin updates also update those files and it replaced the one you used in the beginning.