SLIMS Help

The Solexa Laboratory Information Management System, or SLIMS for short, is designed to allow Solexa users to enter basic information about their Solexa experiments for storage in a backend database. By storing the information in a database it becomes easier to later review, search, and share information about those experiments.

In the SLIMS system there are 2 main types of users- the administrative user (for administrative documentation go HERE), and the regular user. The administrative user is one who is concerned with cataloguing all of the associated information with a Solexa run. They generally have access to or knowledge of the physical experiments, including where the data from that experiment is located. The regular user is one who does not run the experiments, but is mostly just concerned with the results. The regular user is likely a client who has purchased one or more lanes of sequence analysis. They may use SLIMS to get access to data from the experiments that were run for them.

Upon logging into SLIMS, all users are immediately directed to the View Runs page. Depending on the permissions that user has, they will be listed any runs in which they have access to. For each run in that list there is information for the date in which it was run (in YYYY-MM-DD format), the name of the solexa machine that ran the experiment, and any assigned description for the run. In order to see more information about any particular run, the user may click on the "View" link. Note that as long as the user has access to at least 1 of the lanes for an experiment, that run will show up on their View Runs page. Access is further restricted once clicking on the "View" link. An image of the View Runs page can be seen below:

Once the user has clicked on the "View" link from the View Runs page they are sent to the View Run page (seen below). The View Run page has most of the general information about the run available to all users who have any access to this run. This is the information seen on top, including:

Mahine Name
Number of Cycles
The name of the directory that the experiment data is stored in
The date the experiment was run
When the administrative user entered this run information
A brief description as provided by the administrative user

Below this general information is information that is specific to each lane. Here, access is given on a per lane basis. Only if a user has permission to view information about that lane is the lane listed. This is achieved through having certain permissions associated with that lane's assigned Group. With the below image as an example, if a user only had viewing permissions for Luca Comai's group, they would only see information for lanes 3 through 5.

For each lane that a user is listed, they are given basic information such as the group that owns it, the organism sequenced, the primer concentration, and a brief description. Additionally, the user is granted access to the files associated with the lane. These files can be viewed by clicking on the "Files" link, which will bring the user to a page of browsable files and folders. Ofcourse, there are gigs and gigs of data with hundreds of files, and so if a user only cares about the standard files, they can click on the "Summary" link. There they will be given access to a few of the files that they are likely interested in.