SetupX (open technology platform) New version of SetupX is about to be released in the next couple of days. The CVS contains the latest development! If you want to run the last final and stable version checkout Version 421.

svn checkout -r421 http://setupx.googlecode.com/svn/trunk/ setupx-read-only 

SetupX

SetupX is a system that enables investigators to detail and set up a biological experiments.

workflow of the system

SetupX has various functionalities allowing the users to run the experiments and samples smoothly and fast in the lab. In order to give you an impression here is a “typical workflow” of how a sample “travels” through the lab.

First of all the user that is interested in running the samples contacts the PI running the lab equipped with a SetupX system. This will allow them to detail questions about the experiment. Then a user account is created for the new collaborator. Using this account the collaborator logs into SetupX and starts defining the experiment – this has not to be done in one step and just by a single user. An experiment can be modified until the first sample is actually being run on the machine. By sharing the experiment with other researchers certain information can be entered by different people. For example information of the harvest can be more easily detailed by a certain group of researchers who actually did the harvesting while the preparation of the samples can better be detailed by others. The main goal is to have a complete description of the experiment.

After the definition is completed the samples that are labeled with IDs identical to the IDs in the system can be shipped to the lab running the samples. In order to avoid mixing up samples SetupX comes with a label printing software to create chemical and heat resistant labels that can be place right on the vials.

By the time the samples arrive in the lab the operator in the lab checks for completeness of the samples. After storing the samples in the freezer the operator enters this information in SetupX in order to make sure that everyone knows how many samples are waiting in which freezer and also since when the samples are waiting to be analyzed. After the lab operator prepares the samples the information is updated in SetupX again. This continuous tracking allows the users to have a real time view of the lab and its progress.

Next step will be the actual analysis on the GC. Therefore the lab GC operator selects the samples that are going to be run in a menu in SetupX and creates a sequence for the GC. Quality controls, Reagent blanks, Method blanks are automatically added and the samples are randomized.

While the samples are running on the GC the status information of each samples is constantly updated. By the time all samples are completed the data can be taken from SetupX and be sent to connected annotation software. The created result files are available and can be downloaded through SetupX as soon as the annotation software completes the calculation.

Every user that has access to this experiment can now download and use the acquired data. In order to make the data publicly available the system allows the administrator to curate the data received from the annotation software. The curated data is then uploaded back into the system through a wizard. From then on the data is publicly available.

contact

Feel free to contact us.

mscholz@ucdavis.edu

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Installation

(part of the installation documentation)

Setup SetupX

The entire installation of SetupX is distributed via subversion. The Subversion repository contains the most recent stable version of SetupX. In addition you can different prepared installations as ISO images or images for a vmware.

Downloading the newest release

In order to keep your installation up to date the sources are kept in a Subversion repository – it contains the latest version – make sure that your system is kept up to date by refreshing the sources from time to time.

SVN

Check every required data out from the repository by running (it requires that the folder /usr/share/setupx does exist already)

svn checkout http://setupx.googlecode.com/svn/trunk/ /usr/share/setupx

This will get you a local copy of all files required to run your version of SetupX including all required ontologies and taxonomies.

(this is part of the documentation - you will get a copy of the entire document when you check it out)