Question: Data management/annotation solutions for microarray and NGS experiments
gravatar for Adamc
3.6 years ago by
United States
Adamc540 wrote:


I'm trying to figure out if there's an existing system that does what I'm looking for before I go and try to build my own. I'd like to put together a data management system for microarray and sequence datasets, that can be used to store sample annotation, raw data (microarrrays), analysis results (DE gene lists, QC info, PCAs, etc), and other notes. We're not a core and don't have our own sequencer so we don't need the workflow tracking features of most genomics LIMS. We've got over 1000 CEL files sitting in a folder, and desperately need to start associating metadata with them.

I've checked existing relevant threads on this at multiple bioinformatics community sites. Most recently I've looked into BASE and Gnomex, as well as considered using a wiki for the purpose. I don't think a wiki would be quite the right fit. The BASE UI is a little too complex and I think it would scare off our biologists who also want to be able to see what samples we have run. Gnomex could work, but the UI is flash-based, which might cause some issues in the future, since flash is generally being phased out in favor of HTML5. Also, while I like the general organizational scheme that Gnomex uses, it seems like it would get confusing with a lot of attachments to an experiment, or a lot of experiments.

We're not completely averse to commercial solutions- I requested a quote/demo of GeneSifter also- but free/open source is always an easier sell.

Is there anything that I've missed somehow? I just want to make sure I didn't overlook a good solution before I spend a few months building something new (or customizing something like Galaxy).


ADD COMMENTlink modified 3.6 years ago by klemen160 • written 3.6 years ago by Adamc540

Does GEO suits your need?

ADD REPLYlink written 3.6 years ago by Sam2.1k

GEO would not be appropriate- we don't intend to make all the data public, and it's not possible to associate analysis results.

ADD REPLYlink written 3.6 years ago by Adamc540
gravatar for klemen
3.6 years ago by
klemen160 wrote:


I am Klemen from Genialis, and we are developing such software you are looking for. Our platform enables you to organise your data, annotate meta data to it and implement tool for data analysis. It offers a customization of the interface, which meta data you associate to each file and so on. The interface is also biologists friendly, so it is easier for them to look at the data and to see, what has been done, what is the meta data for each file and which analysis were performed. 


In case you are interested to hear more about it and to look at it, please feel free to contact me on my email:


I hope you will find a solution that meets your needs. 

ADD COMMENTlink written 3.6 years ago by klemen160
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