We've just released the first version of a new tool called Labrador: http://www.bioinformatics.babraham.a...ects/labrador/
What it's for
We found that a lot of people were asking us to download and process data from public repositories. Typically, we reprocess this data from raw reads in house. Increasing amounts of our time was being spent digging out download URLs and running the same analyses on different datasets.
Labrador was written to streamline this process. It can track projects and notify users, it automates the retrieval of metadata from public sequence data repositories and it can generate scripts based on this data.
What it does
Labrador has two target groups: end-users (researchers) and bioinformaticians.
Researchers can use Labrador to:
Bioinformaticians can use Labrador to:
Video tutorials
We've made three video tutorials to help you get started with Labrador:
How it works
Labrador is a web-based tool designed to run on a local intranet, written in PHP with a MySQL back end. Labrador communicates with the GEO, NCBI SRA, EBI ENA and the DDJB to automatically retrieve metadata and accession numbers.
Bioinformaticians can manage the processing of datasets and use the retrieved metadata to generate processing bash scripts or download files. This is entirely customisable, allowing you to make Labrador fit in with your existing environment. Labrador comes with a number of common processing pipelines. Once processed, it's easy to view reports within the browser which are associated with the projects and shown in-page.
Where to get it
Labrador is free software under the GPLv3. It is written in PHP and MySQL and we run it on an apache system. You can download Labrador here.
We have been using Labrador at the Babraham Institute for several months and have found it helpful. We're keen to hear any feedback about bugs or suggestions for improvements.
Hopefully Labrador can be a useful tool for some others in these forums!
Phil
What it's for
We found that a lot of people were asking us to download and process data from public repositories. Typically, we reprocess this data from raw reads in house. Increasing amounts of our time was being spent digging out download URLs and running the same analyses on different datasets.
Labrador was written to streamline this process. It can track projects and notify users, it automates the retrieval of metadata from public sequence data repositories and it can generate scripts based on this data.
What it does
Labrador has two target groups: end-users (researchers) and bioinformaticians.
Researchers can use Labrador to:
- Browse and search previously processed datasets
- View processing and analysis reports in their web browser
- Download data through their web browser
- Request new datasets, with required information automatically retrieved from accession numbers
Bioinformaticians can use Labrador to:
- Speed up retrieval of project information from repositories
- Catalogue processing and analysis
- Create automated analysis bash scripts
- Customise templates for analysis script generation
Video tutorials
We've made three video tutorials to help you get started with Labrador:
- End-User Usage Tutorial - A screencast showing basic usage of Labrador for researchers
- Administration Tutorial - A screencast showing administrative use of Labrador for bioinformaticians
- Installation Walkthrough - A screencast showing the installation of Apache, PHP, MySQL and Labrador on a blank server.
How it works
Labrador is a web-based tool designed to run on a local intranet, written in PHP with a MySQL back end. Labrador communicates with the GEO, NCBI SRA, EBI ENA and the DDJB to automatically retrieve metadata and accession numbers.
Bioinformaticians can manage the processing of datasets and use the retrieved metadata to generate processing bash scripts or download files. This is entirely customisable, allowing you to make Labrador fit in with your existing environment. Labrador comes with a number of common processing pipelines. Once processed, it's easy to view reports within the browser which are associated with the projects and shown in-page.
Where to get it
Labrador is free software under the GPLv3. It is written in PHP and MySQL and we run it on an apache system. You can download Labrador here.
We have been using Labrador at the Babraham Institute for several months and have found it helpful. We're keen to hear any feedback about bugs or suggestions for improvements.
Hopefully Labrador can be a useful tool for some others in these forums!
Phil
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