User manual

Because you don't want to be this kind of user...


What is BioRepo ?

The rapid increase of genomics data generation, especially with the expansion of High Throughput Sequencing (HTS) technologies, brings biologists and bioinformaticians to find solutions to efficiently manage and store the resulting amount of data. BioRepo is a Biological data Repository which addresses those needs. Similarly to a Laboratory Information Management System (LIMS), its main goals are to store, manage and share data among collaborators, but also to allow their direct visualisation in genome browsers.


Registration

To access to BioRepo your lab has to be registred in. Send an email to us if you want to test BioRepo.


How to use it

BioRepo offers a data-tracking system with a flexible architecture and a smart data exchange interface. This system is built on three levels : Project, Sample and Measurement.

Create your Project

This is the first logical step. See the Project level as a big folder where you will store all your samples and data (measurements) in.

The Projects page is available for logged users. Here are listed all your personally created projects.

To create a new one, you have to click on "New Project" on the top left and to fill the fields that appear to you.

You are allowed to attach one or several samples to your new project. However, for your first project you will have to create it without any samples (because you have to create them, cf. "Create your Sample").

Warning : you can't attach the same sample to several projects at the same time. One sample is always linked to one and only one project.

Create your Sample

The Sample level allows to save metadata of your experiments. The main metadata field (shared by all the labs in BioRepo) here is the type of your sample (ex: ChIP-seq, RNA-seq, ChIP-chip, ...). Others fields, defined for your lab, can be filled by clicking on "New Sample". You can watch your samples in the Samples page.

A sample can contains one or several measurements.

Create your Measurement

Finally, there is the Measurement level. By clicking on "New Measurement" in the Measurements page you will be invited to upload a file into BioRepo. You will have to fill the different metadata fields to facilitate your future search requests.

A measurement can be attached to one or several samples (use shift/cmd + click).

Privacy :


Different ways to upload your data

You can upload your data to Biorepo from three different sources:

  1. From a local file on your harddisk
  2. From a HTTP link
  3. From a Vital-IT path

Use the internet browser for file size <200Mo

The HyperText Transfer Protocol (HTTP) includes limitations. Among these limitations, there is the response time to the server which can include a "connection timed out" error. To avoid it, please use the BioRepo browser version only for file sizes under 200 Mo.

Use the Excel spreadsheet for the rest

Each registred lab into BioRepo gets its Excel spreadsheet here. Please download yours, fill it and send it back to your BioRepo administrator with the corresponding files in an archive (if local files selected).

The administrator gets access to the BioRepo server and is allowed to upload data this way.

This upload way is useful to add a lot of files at once. Moreover, this saves time.


BioRepo's buttons


Search page

The search page is your best friend to recover old data from an old experiment.

To find a file with it you can use the search buttons customised for your lab on the top of the page. You can also use the free text search on the top-right of the grid.

The grid is live-updated with respect to your search request(s).

It is possible to apply some actions in this page. You can select-by-click the measurement(s) of interest and :


Tree View

You can get a fast and global view of what is into BioRepo for your lab with this page. Try it now !