User details

Click the hyperlink to your user login located in the top left corner to view the details of your account. If you find inconsistencies, please contact the staff of the IIT Genomic Unit.

Filtering and Sorting

All information displayed by the LIMS can be filtered by typing keywords in the text fields below the column header. This feature facilitates finding records of interest. When arrows are displayed close to the column header, the records can be re-sorted by clicking the column header.

Viewing your samples

When you log in and click the Samples menu option, you will see your samples that are currently present in the system. When you click the sample ID header, the samples will be re-sorted by ascending or descending sample ID.

Sample submission

To place a sequencing request, click the New Sample button and fill in all the requested information in the request form. You can modify a request as long as its status is requested. Once the sample has been processed, modifications are no longer permitted.

Project management

You can organize your samples into projects. Clicking the Projects menu option will list your current projects. To see project details, click the Project ID. Projects facilitate finding specific samples. Furthermore, you can add or delete collaborators and set their access permissions to the data.

To create a new project, click the New Project button. Fill in project name and description and click Save. The new project will now be listed in the projects table. Click on the Project ID to add or remove samples and to add or remove collaborators. Hold down the control key for selecting multiple samples. The sample owner will automatically be added to the list of collaborators for the project.

To change permissions of a collaborator, select the collaborator and click Change Permission. The permissions will be toggled between read only and full access. To add a collaborator, click the Add New Collaboration button. Select one or more new collaborators by holding down the control key. Click Add Selected to finish.

Assembling a sequencing run

Sequencing runs are assembled by the sequencing staff. A new run is created by clicking the New Run button on the Runs page. Samples are added sequentially to the run. For each sample, the lane and the sequencing reagents used must be filled in. Once added to the run, the sample status changes to queued.

Virtual flow cell

Before committing a run, the principal investigators involved must give their approval. This is done by clicking the Virtual Flowcell menu option. Here, all the queued samples are displayed. The principal investigator needs to confirm the samples by clicking the Confirm Selected button. The sample status then changes to running and the sequencing run can start.

Samplesheet

The sample sheet is used by Illumina's CASAVA software to demultiplex samples and for converting base call files to FASTQ formatted sequencing data. The corresponding data base table is interrogated by the work flow system to assemble analysis scripts.

Data

Three types of information regarding the data are displayed in separate tabs: Raw Data, Aligned Data, and Annotated Data. The Raw Data table lists the path to the FASTQ data. The Aligned Data table lists the path to bam/bigwig files, the reference genome assembly, the alignment algorithm used, and the parameters used for the alignment.

The Annotated Data table lists the path to annotated alignment data. An annotated alignment is a bed file produced by MACS to call ChIP-Seq peaks or a bed file listing mutations, for example. The algorithm and the parameters used to produce the annotation are listed here.

Users

The Users table lists all registered users and serves administrative purposes.

Reagent

The Reagent menu option lists the currently available sequencing reagents. When an aliquot is used for a sequencing run, the number of available reactions is diminished by 1. The sequencing staff interrogates this table to place orders for new reagents in a timely fashion. New reagents are added by clicking the New Reagent button and filling in the required information.

Logout

Close the current session.

About this Demo version

This is the Demo version of the SMITH LIMS. It is fully functional except that the workflow system is not incorporated for security reasons.

You can see the users that are currently registered with the system. To log in as a user with a given role, type the user login and the password, which is twice the login name.

For example, to log in as admin, type login name admin and password adminadmin. Once logged in, all the functionalities of the LIMS are available but you cannot launch analyses.

Thanks for your interest.

The developers.