News/Intern @ Aniseed: work on Chado
Our team combines various techniques of molecular and cellular biology, bioinformatics, and mathematical modeling to decipher and formalize the embryonic development of animals. The team is composed of experimental biologists and computer scientists.
To integrate these heterogeneous data of gene expression, genomic sequences, anatomical and quantitative description of embryology, we have developed the Aniseed system (Ascidian Network for In Situ Expression and Embryological Data). This sophisticated information system is being rewritten using Chado and then extended.
We are proposing to host up to three students in the team located in the Research Center on Macromolecular Biochemistry (CRBM) in Montpellier. The working language in the lab is English. Internships are paid.
Each intern will work on the development of a new Chado module of Aniseed. The development of each module will include the formalization of biological data and their interactions with data already represented in the database, modification/extension to the schema, use/adaptation of ontologies, and the development of interfaces to graphically represent the data and mine them. The data considered include:
- SELEX-seq DNA-binding specificities for a large fraction of ascidian transcription factors obtained by the team
- Data from ChIP-seq/RNA-seq experiments
- Signal transduction pathways/networks
Development of a module for data curation (manual annotation and verification) is also proposed.
The projects are primarily intended for students with a training in computer science, or biologists who have a very good practice of software development. The candidates are expected to have team spirit, autonomy, dynamism and creativity. Interest in molecular biology is highly desirable, and some basic knowledge of biology would be welcome. Given the international nature of the project, a command of English sufficient to understand technical seminars, annotating code, and present the work is requested. Computer skills required are:
- Knowledge of relational databases (PostgreSQL, MySQL). Knowledge of Chado would be an asset.
- OOP / Languages: PHP 5 (Jelix framework), Perl, XML
- Control of web interfaces PHP / HTML / Apache, IDE: NetBeans
- Experience in web-service (XHTML, HTML, CSS, XML)
- Linux OS