iSkyLIMS description

The introduction of massive sequencing (MS) in genomics facilities has meant an exponential growth in data generation, requiring a precise tracking system, from library preparation to fastq file generation, analysis and delivery to the researcher. Software designed to handle those tasks are called Laboratory Information Management Systems (LIMS), and its software has to be adapted to their own genomics laboratory particular needs. iSkyLIMS is born with the aim of helping with the wet laboratory tasks, and implementing a workflow that guides genomics labs on their activities from library preparation to data production, reducing potential errors associated to high throughput technology, and facilitating the quality control of the sequencing. Also, iSkyLIMS connects the wet lab with dry lab facilitating data analysis by bioinformaticians.

According to existent infrastructure sequencing is performed on an Illumina NextSeq instrument. Data is stored in NetApp mass storage device and fastq files are generated (bcl2fastq) on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for bioinformatics analysis (GALAXY), the iSkyLIMS app, and host the MySQL information tier. iSkyLIMS WetLab workflow deals with sequencing run tracking and statistics. Run tracking passes through five states: "recorded” genomics user record the new sequencing run into the system, the process will wait till run is completed by the machine and data is transferred to the mass storage device; “Sample sheet sent” sample sheet file with the sequencing run information will be copied to the run folder for bcl2fastq process; “Processing data” run parameters files are processed and data is stored in the database; “Running stats” demultiplexing data generated in bcl2fastq process is processed and stored into the database, “Completed” all data is processed and stored successfully. Statistics per sample, per project, per run and per investigation are provided, as well as annual and monthly reports. iSkyLIMS DryLab workflow deals with bioinformatics services request and statistics. User request services that can be associated with a sequencing run. Stats and services tracking is provided.

Installation and usage

For installation and usage instructions please refer to the wiki. For any problems or bug reporting please post us an issue

iSkyLIMS Demo

iSkyLIMS demo is available for your convenience, in a virtual machine image, running on VirtualBox and as a Singularity container.
Download the VM image and/or the container using with your favorite ftp client with the following information:

Server: sftpbioinfo.isciii.es
Port : 50122
user: iskylims
Password: 3skyL3MS_2018

You can also download the virtual machine from this Google drive link

Run VM image on VirtualBox

After successful loging transfer the file demo_iSkyLIMS.ova which it is inside the iSkyLIMS folder.

On the VirtualBox Manager, import the image selecting on the menu

File --> Import.

Once import task is completed, click on the Start icon to run the VM.

For loging to the VM use the following credential:

user: django 
Password : djangoPass

Open Mozilla navigator and it will automatically shows iSkyLIMS homepage located on http://localhost

Log into iSkyLIMS with different roles using the following credentials:

  • As investigator role use the user Eva_user and password iSkyLIMS
  • As wetlab manager role the user is John_manager and password iSkyLIMS
  • If you need to login as django administrator type the url http://localhost/admin using user : admin and password : iSkyLIMS

Run singularity container. (BETA - this method will be improved shorty, but it works for now)

  1. First you need to have installed singularity. Please follow vendor instructions. We recommend using epel package installation as 2.6 version of singularity is enough for our purposes.

  2. Shell into the container (you need to use sudo).

sudo singularity shell iskylims.simg
  1. Start needed services
service smbd start
service mysql start
apachectl -D FOREGROUND
# If you want to play with the image you can execute this last command in foreground.
apachectl -D FOREGROUND &
  1. Open your preferred browser (Firefox or Chome) and type:
localhost

iSkyLIMS website will be shown!! You can explore the website using this two users:

  • bioinfoadm: user inside WetlabManager and Admin_iSkyLIMS groups with manager permissions. (passwd:"iskylims")
  • regular_user01 and regular_user02: regular users with regular permissions.

With bioinfoadm user you can access Admin panel:

localhost/admin

There you can access User table and change regular_user01 and regular_user02 passwords.

  1. Don't forguet to stop the services before exiting the container, it will prevent possible conflicts with your local installation.
    service smbd stop
    service mysql stop
    apachectl stop

Iskylims

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Iskylims Info

⭐ Stars 19
🔗 Homepage github.com
🔗 Source Code github.com
🕒 Last Update a year ago
🕒 Created 3 years ago
🐞 Open Issues 10
➗ Star-Issue Ratio 2
😎 Author BU-ISCIII