Job ID:
Job date: 2015-01-19
End Date:
Company : European Bioinformatics Institute. Country : Role : Faculty
Job date: 2015-01-19
End Date:
Company : European Bioinformatics Institute. Country : Role : Faculty
Job Description:
The Vertebrate Genomes Team seeks an enthusiastic developer to work on comparative genomics for the Ensembl team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Genome Campus near Cambridge in the UK.
Ensembl (https://www.ensembl.org/) is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. Large-scale sequencing projects are now collecting genome sequences from hundreds of new species, and further orders of magnitude will be reached in the next years (for example the Genome 10K project). These data will contribute to improving our knowledge and understanding of the evolutionary history of vertebrate genes and genomes, and the connection between genome evolution and speciation. In light of these new resources, we are looking for an additional member for the team to expand and develop the comparative genomics databases for Ensembl.
The successful candidate will be involved in creating the Ensembl resources as well as maintaining and developing the production pipeline and the associated Perl API.
Reporting to the Ensembl Comparative Genomics Project Leader, the developer's primary task will be to maintain and develop the TreeFam and Gene Trees components of the Ensembl project. This will include working closely with collaborators and keeping up-to-date with scientific research in the area of gene tree reconstruction, including multiple-sequence aligners, clustering frameworks to generate protein family clusters (such as Hidden Markov Models to describe each protein family), and phylogenetic reconstruction of the sequences within each cluster.
Enabling usability of comparative genomics data including the visualisation of such data is critical and this is an area of development within the team. We aim to develop novel methods to summarise and visualise trees encompassing thousands of genes.
In particular, and in addition to the above, this role will involve:
• Maintaining and developing the Ensembl Comparative Genomics pipelines, databases and API.
• Ensuring usability of the Compara gene trees resource including visualisation of gene trees.
• Helping with coordination of the Ensembl comparative genomics release process.
• Supporting the Ensembl Genomes team and other external users in their use of the comparative genomics pipelines, including documentation of standard operating procedures.
• Teaching the usage of the Ensembl Compara API at the quarterly API workshops (https://www.ensembl.info/workshops/)
• Participation in collaborations between Ensembl and research groups/consortia.
• Representing the project and the institute at conferences.
The EBI is part of the European Molocular Biology Laboratory(EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry. EMBL-EBI staff enjoy many benefits including sports facilities, a free shuttle bus to Cambridge and other nearby centres, and an attractive working environment set in 55 acres of parkland.
The ideal candidate will hold a PhD in molecular biology, bioinformatics or a related field or a Masters degree with appropriate experience. Previous experience of working in a production software environment and organising tasks to fit defined release cycles is desirable but not essential.
You will have experience of working in a UNIX/Linux environment and must have programming experience: the ideal candidate will have at least 2 years experience of Perl programming or will have a computational background and a demonstrable knowledge in comparative genomics.
A high proficiency in object-orientated Perl and shell scripting is essential and the post holder will be expected to be comfortable working in a Unix environment working with relational databases. As you will be expected to work on the visualisation of Ensembl Gene Trees, knowledge of (or an interest in) web programming and design and the related common libraries/development patterns would be welcome. Experience of the following would be highly beneficial but not essential:
• Compute gird engines (such as Platform LSF)
• Version control systems, especially GIT
The successful candidate will be self-motivated and capable of working both independently and within a closely interacting team of scientists in an international academic environment. They should be comfortable with detail-orientated work, project deadlines, and enjoy the challenges and excitement associated with working in a fast moving field.
Excellent English, written and oral, communication and interpersonal skills are essential
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.
We welcome applications irrespective of gender and appointment will be based on merit alone. Applications are welcome from all nationalities. Visa information will be discussed in more depth with applicants selected for interview.
Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.
Additional Info:
[Click Here to Access the Original Job Post]
The Vertebrate Genomes Team seeks an enthusiastic developer to work on comparative genomics for the Ensembl team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Genome Campus near Cambridge in the UK.
Ensembl (https://www.ensembl.org/) is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. Large-scale sequencing projects are now collecting genome sequences from hundreds of new species, and further orders of magnitude will be reached in the next years (for example the Genome 10K project). These data will contribute to improving our knowledge and understanding of the evolutionary history of vertebrate genes and genomes, and the connection between genome evolution and speciation. In light of these new resources, we are looking for an additional member for the team to expand and develop the comparative genomics databases for Ensembl.
The successful candidate will be involved in creating the Ensembl resources as well as maintaining and developing the production pipeline and the associated Perl API.
Reporting to the Ensembl Comparative Genomics Project Leader, the developer's primary task will be to maintain and develop the TreeFam and Gene Trees components of the Ensembl project. This will include working closely with collaborators and keeping up-to-date with scientific research in the area of gene tree reconstruction, including multiple-sequence aligners, clustering frameworks to generate protein family clusters (such as Hidden Markov Models to describe each protein family), and phylogenetic reconstruction of the sequences within each cluster.
Enabling usability of comparative genomics data including the visualisation of such data is critical and this is an area of development within the team. We aim to develop novel methods to summarise and visualise trees encompassing thousands of genes.
In particular, and in addition to the above, this role will involve:
• Maintaining and developing the Ensembl Comparative Genomics pipelines, databases and API.
• Ensuring usability of the Compara gene trees resource including visualisation of gene trees.
• Helping with coordination of the Ensembl comparative genomics release process.
• Supporting the Ensembl Genomes team and other external users in their use of the comparative genomics pipelines, including documentation of standard operating procedures.
• Teaching the usage of the Ensembl Compara API at the quarterly API workshops (https://www.ensembl.info/workshops/)
• Participation in collaborations between Ensembl and research groups/consortia.
• Representing the project and the institute at conferences.
The EBI is part of the European Molocular Biology Laboratory(EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry. EMBL-EBI staff enjoy many benefits including sports facilities, a free shuttle bus to Cambridge and other nearby centres, and an attractive working environment set in 55 acres of parkland.
The ideal candidate will hold a PhD in molecular biology, bioinformatics or a related field or a Masters degree with appropriate experience. Previous experience of working in a production software environment and organising tasks to fit defined release cycles is desirable but not essential.
You will have experience of working in a UNIX/Linux environment and must have programming experience: the ideal candidate will have at least 2 years experience of Perl programming or will have a computational background and a demonstrable knowledge in comparative genomics.
A high proficiency in object-orientated Perl and shell scripting is essential and the post holder will be expected to be comfortable working in a Unix environment working with relational databases. As you will be expected to work on the visualisation of Ensembl Gene Trees, knowledge of (or an interest in) web programming and design and the related common libraries/development patterns would be welcome. Experience of the following would be highly beneficial but not essential:
• Compute gird engines (such as Platform LSF)
• Version control systems, especially GIT
The successful candidate will be self-motivated and capable of working both independently and within a closely interacting team of scientists in an international academic environment. They should be comfortable with detail-orientated work, project deadlines, and enjoy the challenges and excitement associated with working in a fast moving field.
Excellent English, written and oral, communication and interpersonal skills are essential
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.
We welcome applications irrespective of gender and appointment will be based on merit alone. Applications are welcome from all nationalities. Visa information will be discussed in more depth with applicants selected for interview.
Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.
Skills :
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Additional Info:
[Click Here to Access the Original Job Post]