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Old 06-03-2013, 11:02 PM   #1
sklages
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Location: Berlin, DE

Join Date: May 2008
Posts: 611
Smile Open Source LIMS: openBIS or GNomEx

After investigating some time in searching for a free LIMS well suited for NGS (some HiSeqs2500, optionally some 454) I found two systems to be a potential candidate.

openBIS [1]
GNomEx [2]

I was wondering if someone has one of these systems running (in daily routine). Before running some "deep tests" I'd like to gather some experiences, some "pros" and "cons", advantages or disadvantages.

Other (lightweight) LIMS like Sierra or Galaxy-LIMS are nice but too lightweight ;-)

Any comments?

[1]=http://www.cisd.ethz.ch/software/openBIS
[2]=http://sourceforge.net/projects/gnomex/
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Old 09-01-2013, 02:07 PM   #2
DRYTCYV
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Location: Portugal

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Hi,

Any feedback?
Some months ago i asked about Gnomex feedback (in LinkedIN) and someone told me about some bugs, and that was a reason to uninstall it.
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Old 09-01-2013, 10:19 PM   #3
sklages
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Hi,

well, bugs, OK not very uncommon. I tried Gnomex last year and was quite disappointed concerning support (or any feedback/help) and documentation. Currently I am testing MISO (http://www.tgac.ac.uk/bioinformatics...ormatics/miso/) which looks very promising. The developers are nice and very helpful ...
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Old 05-29-2014, 05:05 PM   #4
tdisera
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Location: Salt Lake City, Utah

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Default GNomEx improvements

I am the principal developer of GNomEx. We now have a full development team devoted to improving the application. The documentation has improved and the install is less error-prone. I'd appreciate any feedback from folks who have tried it out in the last year. Although we are focused on meeting our core facility's needs, it is always helpful to hear where the software falls short and excels. Thanks!
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Old 05-26-2015, 05:35 AM   #5
clolalan7
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Location: Michigan

Join Date: May 2015
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Default GNomEX install

Good morning,

I am currently investigating the available LIMS for our new Epigenomics core, and GNomEX is one that I find interesting.

I have spent a great deal of time trying to install it over the long weekend. I cannot say I am an expert, but I have installed a couple of open-source applications and I think the instructions still require improvements. At best, they look like a copy/paste of the settings at the Utah university.

I think the tool looks really great (from the images I have seen and the guest login I used). But at the moment, the install is making me consider the other possibilities.
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Old 10-28-2016, 07:12 AM   #6
Hoxus
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Location: France

Join Date: Sep 2015
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Hi,

I have tried some LIMS, and my best choice are (not sorted): MISO, GNomEx and openBIS.

openBIS is really simple to install (push button).
MISO and GNomex are a bit more painful.

I write here, after long time, because I find this post with google with Gnomex keyword.
I just finish to "install" Gnomex:
- after changing some file permissions, it's start... a bit.
- after adding j4log java jar file, it's start more.
- by now, I can log me, and I see a progress bar screen, and it's stop with message "There has been a system error, please try the request again".

Catalina logs say me that this error is SQL related, about an unknown column 'librarypre0_.codeRequestCategory' in 'field list'.

Gnomex developpers have made a fabulous work, and I can't code 1% of that.
But I don't manage to find any way to contact them with an issue/contact form. I will search again, about the error and about Gnomex developpers, and I will try to write an email directly.

edit :
I just found an form in sourceforge.

Thks

Last edited by Hoxus; 10-28-2016 at 07:18 AM. Reason: found an issues form in sourceforge
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