Recent Posts

Hi,

I've had the same problem. In my case the solution was to start J-Express from the command line (double-clicking the icon would for some reason use 32-bit java):

first cd to the folder where J-Express is installed, then
"C:\Program Files\Java\jre6\bin\java.exe" -jar Launch.jar

Hope this is of help.

Torben

The name of the folder inside PW is mmu. The "genome" and "map_title.tab" files are also under PW.

It actually worked yesterday, after I had copied the files from my colleague (these files were from last October). But when I tried again today the pathways were disappeared from "Pathway set".

Yes, I also tried closing and reopening the pathway window after downloading.

Is the appearance of the pathways dependent of the selected dataset? Because I dont remember which dataset I had selected when it worked.

Ane

Hi, can you give me some more information?

have you tried closing and reopening the pathway window after downloading the pathway?

What is the name of your new folder (inside the PW folder)? do you have a "genome" and "map_title.tab" file there?

regards,
Bjarte

I have the same problem.

There is nothing to select under "Pathway set", even though I have downloaded the files and they they seem to be in the correct folder.
Do you have any more suggestions?

Where on the Kegg webpage can I find Kegg IDs to download and put in my data set with ID linker, if this is the problem?

Ane

Hi,

If the pathway files are put in the correct folder (the one pecified under settings -> options ->files and folders), they should be picked up automatically by J-Express..
To use them, open the pathway analysis and select the correct pathway set in the set dropdown box.

If the set are still missing from the dropdown list, your pathway files are probably damaged by for instance an interrupted download, or J-Express does not have the permission to load them.

regards,
Bjarte

Hello,
I am new to J-express, so I don't know if I'm doing something wrong, but I cannot seem to download pathways in the "pathway analysis section". There are no pathways available to begin with.

When clicking "Download pathway" I get a window with the following information:
FTP location: ftp.genome.jp
Path to pathways. /pub/kegg/pathway_gif
Path to genes:

Available sets: (noting)
Downloaded sets: hsa

What am I doing wrong?


Kristina


P.S I see in the download path, that the files are indeed located on my C drive. Bu how to connect these to the J-express software?

Hi Bjarte,
Using java -version I got the following:
Java version "1.6.0_18"
Java(TM) SE Runtime Environment (build 1.6.0.1_18-b07)
Java HotSpot(TM) 64-bit server VM (build 16.0-b13, mixed mode)

quite similar to yours I belive, except the server version.

I also reinstalled Java (latest 64-bit version) in case there were something wrong, but this did not change the limit of approx 1500 MB were J-express refused to start.


Sincerely,
Bjørn Olav

Hi Bjørn,

I am running J-Express successfully on a Vista64 OS with more than 3GB memory..
It seems to me that you are using a 32 bit java VM where the memory limit is around 1.5 GB. If you open a command prompt and write java -version, what is the response?

On my computer I get:
java version "1.6.0_13"
Java(TM) SE Runtime Environment (build 1.6.0_13-b03)
Java HotSpot(TM) 64-Bit Server VM (build 11.3-b02, mixed mode)

Unfortunately I am not using Windows7 myself so I cannot help you switching from 32 bit to 64 bit.. Perhaps there is something you can use here: http://windows7themes.net/windows-7-java-64-bit-download.html ?

regards,
Bjarte

Hi,
I have a computer with 12 GB of RAM (Win 7 Professional 64-bit) and want J-express to utilize as much of this RAM as possible.

However, when I adjust "memusage" in exec.properties gradually up from default 516 MB, J-express refuses to start above approx 1500 MB.

This could be a win/Java setting (this occurs in XP, Vista and win 7 (32 and 64-bit)), and if anybody knows how to fix this I would appreciate all tips!

Yours sincerely,
Bjørn Olav Kvamme

Thanks to your assistance, I was able to export info field data in the correct order.
Thank you very much for your advice.