Exemples d'emplois en bioinformatique

Sources : Linkedin / EBI / Van Andel Institute / Lawrence Berkeley Lab / Nature jobs / SIB / RIKEN / Job Finder USA

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Open position : Bioinformatics scientist (January 2017)

  • Location : Harvard (Cambridge) campus

Job Description

We have two new open positions in the group. We are looking for a bioinformatics analyst and a scientific software engineer to join the teams that develop the HMMER and Infernal software packages for biological sequence analysis.

The teams are growing, with a key new team member Nick Carter, who joined us from high performance computing research at Intel and a previous computer science faculty position at U Illinois. We're aiming in particular to bring out the next release of HMMER, the long-fabled HMMER4. These positions offer the short-term opportunity to help us bring these existing projects to the next level, and a longer-term opportunity to participate in a variety of fundamental computational biology algorithms research and software development.

The scientific software engineer

will work most closely with Nick and myself on HMMER, and later on Infernal in collaboration with Eric Nawrocki (NIH/NCBI). Our codebases are ANSI C99, we take advantage of SIMD vectorization instructions on multiple platforms, and we're working hard on parallelization efficiency with multithreading (POSIX threads) and message passing (MPI), so we're looking for someone with expertise in these technologies. We currently work primarily on Apple OS/X and Linux platforms ourselves, but our code has to build and work on any POSIX-compliant platform, so we're also looking to expand our automated build/test procedures.

Our codebases are open source and we work with standard open source tools such as git, autoconf, and GNU make, and development is distributed amongst a small group of people throughout the world, especially including collaborators at NIH NCBI, U Montana, HHMI Janelia Farm, and Cambridge UK; you can see our github repos here.

The official advertisement for the position is online here, with instructions on how to apply.

The bioinformatics analyst

will work most closely with our bioinformatics secret agent man Tom Jones, Nick, and myself. We're looking for someone to bridge the gap between the computational engineering and the biological applications, someone who will have one hand in the development team (working on how our command line interfaces work, and how our output formats come out), and another hand on our collaborations within Harvard and with the outside world using and testing our software on real problems. We want someone thinking about benchmarking and testing, with expertise in a scripting language (Python, Perl); we want someone working on user-oriented documentation and tutorials (Jekyll, Markdown); we want someone thinking about ease and elegance of use; we want someone working on how our tools play well with others, including Galaxy and BioConductor, and liasing between us and the various package managers who bundle our software (such as Homebrew, MacPorts, all the various Linuxen). The official ad and instructions to apply are online here.

We are reading applications now, and will accept applications in a rolling fashion for at least another month or so; beyond that depends on how our candidate pool looks. The positions are available immediately. Our funding for them has just activated, supported by the NIH NHGRI under the NIH's program (PA-14-156) for Extended Development, Hardening and Dissemination of Technologies in Biomedical Computing, Informatics, and Big Data Science; we gratefully acknowledge this new support, as I've rejoined the NIH community after ten years away at a monastery.

Open position: Bioinformatics scientist (January 2017)

  • Location : Harvard (Cambridge) campus

Job Description

Michele Clamp is building up Harvard's bioinformatics team on the college (Cambridge) campus, and she's got an open position in collaboration with Susan Mango's group:

The Mango Lab in the Harvard Department of Molecular and Cellular Biology in collaboration with the FAS Informatics Group seek a bioinformatician for genomics analysis.

The successful candidate will primarily focus their work on the Mango lab, while embedded within a cohort of informaticians who develop and apply cutting edge approaches to a range of biological questions. Current projects within the Mango lab use genomics to study transcriptional regulation and chromatin dynamics during development. ChIP-seq, FAIRE-seq, RNA-seq, Oligopaint etc. are used to probe the chromatin landscape as cells transition from pluripotency to cell-fate commitment, and the successful candidate will collaborate with lab members to analyze the datasets. The remaining effort will be used to support groups in the Faculty of Arts and Sciences (FAS) that use genomic approaches such as ATAC-seq, Chip-seq, FAIRE-seq, and related methodologies. This will include consulting with faculty groups, teaching workshops on statistical and informatics approaches for understanding these methods, and developing best practice recommendations and benchmarks.

For more information, or to apply

Three positions EMBL-EBI (June 2016)

  • Location : EMBL-EBI Hinxton near Cambridge, UK
  • Category : Staff Member
  • Grading : 5 or 6 (monthly salary starting at £2,475 or £2,769 free of UK income tax plus mobility and other allowances where applicable)
  • Closing Date : 07.08.2016

Bioinformatician 1

  • Contract Duration : 3 years

Bioinformatician 2

  • Contract Duration : 2 years and 11 months

Web Developer

  • Contract Duration :3 years

Job Description - Bioinformatician 1 : We are seeking to recruit a highly motivated Bioinformatician with a keen interest in RNA biology to work at the European Bioinformatics Institute (EMBL-EBI).

You will be working on RNAcentral, a database of non-coding RNA sequences which provides a single entry point for accessing RNA data from an international consortium of RNA databases. You will be a member of the RNA Resources team, which is part of Rob Finn's Sequence Families team, and report to the RNA Resources Project Leader, Anton Petrov. You will work with a team of 4 other people that ensure timely update and release of the RNA Resources, RNAcentral and Rfam.

The successful candidate will be responsible for performing regular database updates, development of new data import pipelines, and implementation of algorithms for mapping RNAcentral sequences to genomes. This postholder will also improve the RNAcentral software infrastructure and develop methods for quality control and data standardisation. The work will require conducting independent research projects and keeping up to date with the field of RNA biology. These research outcome may then be translated to new features within the RNAcentral resource.

Qualifications and Experience You will have a MSc degree (or higher) in Biology, Bioinformatics or a related field with a demonstrated track record of developing bioinformatic pipelines.

Essential Qualifications and Experience

Knowledge of RNA Biology, such as understanding of different types of ncRNAs and their structure
Advanced knowledge of scripting language, ideally Python
Good knowledge of relational databases and SQL
Confident use of git and GitHub
Experience with high-performance computing environments, e.g. LSF or Grid Engine
Experience of data management and data integration
Experience with producing project-specific and general user documentation
Ability to apply best software development practices
Demonstrable research track record

Desirable Qualifications and Experience

Web development experience
Experience with Oracle and PL/SQL
Experience with Docker and VMs
Knowledge of the Perl and Ensembl Perl API a plus
Peer-review publications relating to RNA biology
Experience with managing social media accounts and providing user support

The successful candidate will have strong critical thinking skills and will be able to work both accurately and quickly to meet deadlines. Good communication skills (verbal, presentational and written) are also essential. The postholder will also be expected to participate in team meetings, covering a broad subject range.

Job Description - Bioinformatician 2 : We are seeking to recruit a highly motivated Bioinformatician with a keen interest in structural biology of proteins to work at the European Bioinformatics Institute (EMBL-EBI).

The position will bridge between the PDBe team, run by Sameer Velankar, and the InterPro team, run by Rob Finn, both based at EMBL-EBI. Time will be spent equally working in both teams during the period of work. The successful candidate will also be responsible for working with our partner resource Genome3D to improving the consistence and coherence of structural classifications and to ensure that these data are propagated into the InterPro and PDBe resources. Furthermore, the position will help integrate the structure predictions contained within Genome3D to the respective EBI databases. By nature of this collaborative project, the post-holder will be interacting with two large teams (approximately 25 people in total), as well as liaising with and progress reporting to the Genome3D resource counterparts based as UCL, London.

The successful candidate will be responsible for continuing the established PDBe workflow for cross-mapping different structural classifications, in collaboration with Genome3D /CATH. The post holder will also develop new data exchange protocols and implement update mechanisms for incorporating Genome3D data within PDBe and InterPro. They will then help drive the elaboration of PDBe/InterPro web pages to display these new data types. In conjunction with the EBI training team, the post holder will help develop electronic training material, detailing the new features produced through this work.

Qualifications and Experience You will have a MSc degree (or higher) in Bioinformatics or a related field with a demonstrated track record of developing bioinformatic pipelines.

Essential Qualifications and Experience

Knowledge of structural biology and protein classifications
Advanced knowledge of scripting language, ideally Python
Good knowledge of relational databases and SQL
Experience of consuming RESTful APIs
Web development experience
Confident use of git and GitHub
Ability to apply best software development practices

Desirable Qualifications and Experience

Knowledge building interactive visualisations using SVG or Canvas
Experience working within a team and agile development approaches
Practiced in producing project-specific and general user documentation
Experience with providing user support
User of social media for disseminating science

The successful candidate will have strong communications (verbal, presentational and written) and organisational skills. They must be able to work both accurately and quickly to meet deadlines, as well as be self-motivated and critically thinking. The post holder will also be expected to participate in team meetings, covering a broad subject range.

Job Description - Web Developer : We are looking to recruit an experienced Web Developer to work at the European Bioinformatics Institute (EMBL-EBI).

You will be working on RNAcentral, a database of non-coding RNA sequences which provides a single entry point for accessing RNA data from an international consortium of RNA databases. You will be a member of the RNA Resources team, that is part of Rob Finn's Sequence Families team, reporting to the RNA Resources Project Leader, Anton Petrov. You will work with a team of 4 other people that ensure timely update and release of the RNA Resources, RNAcentral and Rfam.

The successful candidate will be responsible for maintaining and developing the RNAcentral website, including implementation of new interfaces. They will be well-versed in modern web technologies, focused on user experience, and ready to work in an interdisciplinary setting. More specifically, the postholder will improve RNAcentral search functionality, develop interactive visualisations for RNA 2D/3D structure, and enhance the performance and scope of the RNAcentral API. The work will also involve developing web components for embedding RNAcentral data and services on third-party websites.

You will have a BSc (or higher) degree in Computer Science or a related subject and a demonstrated experience in full-stack web application development.

Essential Qualifications and Experience

Advanced knowledge of Python and Django framework
Extensive knowledge of JavaScript and modern frameworks, such as AngularJS
Experience with Bootstrap framework
Confident use of git and GitHub
Good knowledge of relational databases and SQL
Experience building interactive visualisations using SVG or Canvas
Experience with continuous integration and testing tools (Travis CI, Jenkins, Selenium)

Desirable Qualifications and Experience

Knowledge of the front-end ecosystem (React, Gulp, Node, Browserify, Sass etc)
Experience with deployment and monitoring tools (Fabric, Supervisor)
Experience with Docker and VMs
Experience with managing social media accounts and providing user support
Experience working within a team and agile development approaches
Knowledge of RNA Biology a plus

The successful candidate will have strong critical thinking skills and will be able to work both accurately and quickly to meet deadlines. Good communication skills (verbal, presentational and written) are also essential. The postholder will also be expected to participate in team meetings, covering a broad subject range.

Additional Information

  • Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.
  • EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
  • This position is limited to the grant duration specified.
  • Applications will close at 23:00 GMT on the date listed above.
  • It is envisaged that interviews will take place in the week commencing 08.08.2016

Bioinformatician (2 positions) (June 2016)

  • Location : EMBL-EBI Hinxton near Cambridge, UK
  • Category : Staff Member
  • Contract Duration : One 3 year project role, one 2 year project role 5/6 - according to skills and experience. (Monthly salary starting at GBP2475 after tax, plus mobility and other allowances where applicable).
  • Grading : 5 or 6 (monthly salary starting at £2,475 net of tax plus mobility and other allowances where applicable)
  • Closing Date : 11th July 2016

Job Description : We are looking for experienced bioinformaticians to join the Open Targets team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.

Open Targets is a recently established public-private initiative between the EBI, GlaxoSmithKline, Biogen and the Sanger Institute to combine large-scale genomic experiments with objective statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases.

We have two vacancies for experienced bioinformaticians working on large-scale biological data analysis and integration for target identification and prioritisation within the core Open Targets team.

You will join the Open Targets team developing the data processing and database infrastructure to provide the cord deliver of the centre , a genome-wide database of target validity.

Your responsibilities will include

  • development and refinement of suitable data feeds from databases within and outside the partnership including interaction with other groups
  • establishment of automated processing pipelines and quality control procedures, as well as exploratory data analysis in the area of target prioritisation
  • and the role will involve extensive interaction with backend database developers to refine and test the data processing pipeline.

Reporting to the Open Targets Scientific Director you will work together with one other bionformatician.

Qualifications and Experience

You will hold a PhD or MSc in computational biology, bioinformatics, or other computational science and have some previous experience in bioinformatics, database technologies and genome-wide biological data analysis.

We are looking for someone with experience of working in a continuous deployment environment with source control and managed releases. You will have a proven track record of working on large-scale data analysis projects and an understanding of the challenges posed by collaborative projects including flexibility, tight deadlines, and use of state-of-the-art approaches. With excellent interpersonal and organisational skills, you will enjoy working in a highly collaborative agile team, interfacing with other backend developers, web developers and a UX designer.

Experience in software development with Python in a similar role will be an advantage, as will experience with biomedical ontologies and associated tools.

Previous exposure to the following technologies is desirable: REST API, Elasticsearch, Docker.

Additional Information

  • Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.
  • EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
  • This position is limited to the grant duration specified.
  • Applications will close at 23:00 GMT on the date listed above.

Software Developer EGA (May 2016)

  • Location : EMBL-EBI Hinxton near Cambridge, UK
  • Category : Staff Member
  • Contract Duration : 3 years
  • Grading : 5 or 6 (monthly salary starting at £2,475 net of tax plus mobility and other allowances where applicable)
  • Closing Date : 26 June 2016

Job Description : The European Genome-phenome Archive (EGA) are looking to recruit an enthusiastic, highly motivated Software Developer to work an interdisciplinary team at the European Bioinformatics Institute (EBI).

The EGA runs one of the world's largest controlled-access genomic databases with over several petabytes of data stored. We offer an attractive working environment with the opportunity to work on big-data projects and associated technologies with collaborators worldwide.

The successful applicant will work with a focused team of developers to deliver, maintaining and extending the current pipelines and APIs for our global life sciences user communities. You will implement scalable databases, ETL pipelines as well as java library and REST APIs for the management of genetic data and meta-data. The post will require the use of Confluence, Jira and Git in a team programming environment.

You will also engage extensively in both internal and collaborations and will have the opportunity to gain expertise both in terms of technical software engineering and biological scientific data modelling.

Qualifications and Experience

You should hold a bachelors or higher degree in computer science or bioinformatics. Research experience in genomics and bioinformatics is highly desirable - otherwise a keenness to learn the biological domain area while on the job is necessary. The ideal candidate would also have experience of encryption, secure data transfer and networking.

The successful candidate will have experience in production Java programming, including core libraries, JSON parsing, and REST API programming, as well as proficiency in one or more scripting languages (Python or Perl) and Unix command line programming. Experience with relational databases is required, and knowledge of procedural languages such as PL/pgSQL would be advantageous. Prior work experience within a software development team supporting production systems in an academic or commercial setting would be advantageous.

The ability to work within a team is critical to this position and excellent communication skills are essential. The software developer will be required to communicate technical documents, take part in the daily scrum and paired development, as well as provide user orientated communication with external and internal users of the systems. An ability to work to tight deadlines is essential as are excellent English language skills.

Additional Information

  • Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.
  • EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
  • This position is limited to the grant duration specified.
  • Applications will close at 23:00 GMT on the date listed above.

Three positions at Chemogenomics team (ChEMBL-EBI) (May 2016)

  • Location : EMBL-EBI Hinxton near Cambridge, UK
  • Category : Staff Member
  • Grading : 5 or 6 (monthly salary starting at £2,475 or £2,769 free of UK income tax plus mobility and other allowances where applicable)
  • Closing Date : 12 June 2016

Data Mining and Analysis Scientist

  • Contract Duration : 2 years

Scientific Programmer

  • Contract Duration : 3 years

Web Developer

  • Contract Duration :3 years

Job Description - Data Mining and Analysis Scientist : We are seeking a highly motivated data mining and analysis scientist to join the Chemogenomics team (ChEMBL) at the European Bioinformatics Institute (EMBL-EBI). The role is to develop novel computational methods to help in the prediction and understanding of cardiac and hepatic toxicities in support of the EU FP7 funded project HeCaTos.

Reporting to the ChEMBL team leader, the job responsibilities will include:

Data analysis and development of novel predictive approaches To develop novel algorithms to index and analyse toxicology data, and then test these approaches against project data, and public domain validation sets.
To work with other collaboration partners to develop prediction methods, software workflows and new software, including the validation, documentation and training/dissemination of newly developed methods.
To engage in broader dissemination activities for the HeCaTos project and on ChEMBL tools in general

Qualifications and Experience

  • The ideal candidate will hold a PhD (or equivalent) in chemical, biological, biomedical sciences, or a suitable area of computer science. This experience will be coupled with a broad knowledge of the major relevant informatics resources and predictive approaches (e.g. QSAR, data-mining, classification methods, etc.). Of special interest would be experience in the application of such techniques to toxicology data, and knowledge of the general mechanisms of drug toxicity/side effects.
  • The work will primarily involve the development of novel new methods to predict the potential toxicity of novel compounds as well as the development of target prediction methods, annotation of likely functional effects, etc. Hence experience with a number of data analysis/predictive model development tools and methods is desirable (e.g. R, the PyData stack etc).
  • Programming skills (e.g. perl/python, java, C) and familiarity with database querying (SQL) and UNIX is required. Experience in using biological ontologies and text mining methodologies is also desirable. In addition, familiarity with a range of bioinformatics, cheminformatics and drug discovery tools and resources would be advantageous.
  • Due to the interdisciplinary nature of the project, (s)he will be expected to liaise directly with data producers, and software developers/users at other institutes in the collaboration. The work will involve a significant amount of interaction with scientists from many distinct backgroundsGood communication (verbal and presentational) skills are thus essential as is the ability to work both as part of a team and independently. (S)he should be self motivated with a driver for quality, the ability to deal appropriately with confidential data, and work to strict delivery deadlines. Some travel to attend collaboration meetings may also be required.

Job Description - Scientific Programmer : We are seeking a highly motivated DevOps developer to join the Chemogenomics team (ChEMBL) at the European Bioinformatics Institute (EMBL-EBI). The role is to develop software infrastructure to create a reliable ChEMBL data releases through build, package, test, and deployment automated processes.

Reporting to the ChEMBL team leader, the job responsibilities will include:
Improving ChEMBL software infrastructure for ease of deployment, scalability and fault-tolerance
Development and automation of methods for chemical and biological data validation, curation and standardisation
Development of pipelines for the integration of data from internal and external drug discovery resources
Creating clean, well structured, high quality deployment, monitoring and application management scripts
Establishing a culture and environment where building, testing, and releasing data/software, can happen rapidly, frequently, and more reliably
Release management (planning, gate-keeping)
Written and verbal communication (e.g. reporting results, preparing release notes and user guides)
Working towards Continuous Delivery (approach in which the team produce data/software in short cycles, ensuring that the software can be reliably released at any time)

Qualifications and Experience : You will have a BSc (or equivalent) in Computer Sciences, Life Sciences or related discipline with strong programming skills and a proven track record in developing software.

Essential Qualifications and Experience
A minimum of 3 years of professional development experience;
Strong critical thinking and problem solving skills
Experience of developing software on Linux systems
Good experience with a number of scripting languages e.g., Python, Ruby, Bash, Groovy
Knowledge of RDBMS (Oracle, PostgreSQL and MySQL)
Experience of data management and data integration
Use of Git or other source code management tools;
Comfortable with using a wide variety of technologies and tools
Experience with testing and deployment tools
An experience in maintaining GNU/Linux packages, (rpm/yum, dpkg/apt)

Desirable Qualifications and Experience
A MSc in Computer Science, Bioinformatics or Cheminformatics (or equivalent)
Knowledge of cheminformatics/bioinformatics tools and resources (e.g., RDKit, ChemAxon, Pipeline Pilot, BLAST, UniProt, Protein Data Bank)
Experience working with Life Science or Drug Discovery data
Experience in deploying and consuming RESTful web services
Experience with continuous integration tools (Jenkins, Travis-CI)
Knowledge of software deployment tools (Ansible, Puppet, Packer) a plus
Experience with Docker and VMs

The successful candidate will be able to work both accurately and quickly to meet deadlines. Depending on the tasks involved, (s)he will need to be able to work both as part of a team, in close collaboration with other members of the multi-disciplinary Chemogenomics Group, and independently. Good communication skills (verbal, presentational and written) are also essential.

Job Description - Scientific Programmer : We are seeking an outstanding web developer to join the Chemogenomics team (ChEMBL) at the European Bioinformatics Institute (EMBL-EBI). The role involves the design, building, and maintainenance of websites for various projects within the team. (ChEMBL Web Services)

Reporting to the ChEMBL team leader, the job responsibilities will include:
Building accessible and responsive web sites and web applications
Developing new user-facing features
Following established best practices in the web development
Testing websites and identifying any technical problems
Optimizing applications for maximum speed and scalability
Maintaining existing websites
Ensuring that all code is clear, concise, well-documented, tested and stored in a version control system

At EMBL-EBI, we help scientists realise the potential of 'big data' in biology by enabling them to exploit complex information to make discoveries that benefit mankind.

Qualifications and Experience : You will have a BSc (or equivalent) in Computer Sciences or a related subject e.g. Information Technology, Software engineering, Web design. You will have a proven track record in developing web interfaces and an understanding of the best practices in modern web development.

Essential Qualifications and Experience
A minimum of 2 years of professional web application development experience
Proficient understanding of web markup, including HTML5
Excellent knowledge of modern CSS techniques and experience with a CSS Pre-processor such as Sass
Experience with the Django framework and Python scripting
Extensive knowledge of front end technologies: JavaScript, Responsive Web Design, MVC design pattern, REST, Ajax
Building responsive Single Page Web Applications using modern front-end JavaScript technologies like Backbone or Angular
Proficient in the use of code versioning tools, such as Git
Good knowledge of relational databases and SQL
Good understanding of Test Driven Development
Knowledge of emerging web technologies

Desirable Qualifications and Experience
Experience with static page generators (Jekyll, Nikola)
Some Ruby on Rails experience
Some experience with Groovy
Experience with web applications testing platforms and tools (Selenium, Casper.js)
Experience with CoffeeScript a plus

The successful candidate will be able to work both accurately and quickly to meet deadlines. Depending on the tasks involved, (s)he will need to be able to work both as part of a team, in close collaboration with other members of the multi-disciplinary Chemogenomics Group, and independently. Good communication skills (verbal, presentational and written) are also essential.

Additional Information

  • Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.
  • EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
  • This position is limited to the grant duration specified.
  • Applications will close at 23:00 GMT on the date listed above.
  • It is envisaged that interviews will take place in the week commencing 20.06.2016

Full-stack Software Engineer (May 2016)

  • Location : EMBL-EBI Hinxton near Cambridge, UK
  • Category : Staff Member
  • Contract Duration : To 31.12.2018
  • Grading : 5 or 6 (monthly salary starting at £2,475 or £2,769 free of UK income tax plus mobility and other allowances where applicable)
  • Closing Date : 29 May 2016

Job Description : We are seeking to recruit an enthusiastic, highly motivated Full-stack Software Engineer to work at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.

You will be working in the Technology Science Integration group led by Steven Newhouse, the Head of Technical Services, on an internal project to improve the functionality offered by EBI's Tools web interface to offer more storage and workflow options. This work may include:

Deploying, developing and integrating technologies to provide web access to EBI's Tools
Evaluating new tools and technologies for integration into our service offering coming from the open-source communities
Assisting development teams in troubleshooting production issues
Assisting in migrating existing applications to new technology
Developing and extending internal tools to streamline and automate workflows

You will be working with members of EMBL-EBI's Technical Services Cluster (to integrate your software with the other services being operated at EMBL-EBI and from other service providers) and with internal and external users (to gather their initial requirements and support their use of your software) supported through internally and externally funded projects.

Qualifications and Experience

You will have a bachelor's degree or higher in computer science, software development or have equivalent experience and demonstrated experience in full-stack web applications development (i.e. back-end and front-end tiers, including web-based clients, programmatic access APIs, and data access layers). Experience designing relational and non-relational data models is important. Java technologies and frameworks (e.g. Spring) are widely used within the organization, so experience is required, together with modern component-based front-end technologies (e.g. Angular). Scripting language experience such as Perl/Python is also desirable.

Prior work experience should include four or more year's software development in a team environment and supporting production systems in an academic or commercial setting. The ability to work within a team is critical to this position and excellent communication skills, verbal and written, are essential. The software engineer will be required to communicate technical documents, take part in the daily Scrum, as well as provide user orientated communication with external and internal users of the systems. An ability to work to tight deadlines is essential as are excellent English language skills and the ability to work with minimal direction when making technical decisions.

Required

Degree level or equivalent qualification/experience in computational, or related scientific discipline;
At least 4 or more years' experience writing production quality software, ideally in an open development model;
Expert knowledge of Java and Spring (MVC, Security, Integration);
A good knowledge of modern front-end technologies such as AngularJS;
Use of version control (e.g. Git, subversion) and notions of Continuous Integration is important;
Experience with computing infrastructure (e.g. Java web containers such as Tomcat) and working with relational and non-relational databases e.g. MongoDB, PostgreSQL, Oracle or MySQL;
Experience in communicating and working with expert users (e.g. in a science community) in a co-development model.

Desirable

Previous experience evaluating open-source software and its subsequent integration to a production system;
Familiarity with agile development practices and the full software development lifecycle in a team environment;
Knowledge of scripting languages such as Perl/Python;
Experience with VM and/or container deployment in public or private cloud environments;
Experience of working within a dev/ops environment.

You will be able to pay attention to detail but also meet deadlines. You will also demonstrate innovation and a willingness to take on new challenges. You will have a passion for code development and making software that can be used. You have the knowledge and experience to make technical decisions with minimal supervision.

Software Developer / Bioinformatician (March 2016)

  • Location : Heidelberg, Germany
  • Category : Staff Member
  • Contract Duration : 3 years
  • Grading : 4, 5 or 6, depending on experience and qualifications
  • Closing Date : 12 May 2016

Context : The European Molecular Biology Laboratory (EMBL), one of the highest ranked scientific research organisations in the world, is seeking a highly motivated software developer to join the Genome Biology Computational Support (GBCS) team. At GBCS, we use cutting-edge technologies to develop and provide genomics data management and analysis solutions to EMBL scientists.

Are you a skilled DevOps, eager to learn new technologies, curious about cutting-edge bioscience, willing to work in a flexible, collaborative and international environment ? If so, we are waiting for you!

Job Description : The position primarily involves the maintenance and development of emBASE, an EMBL-wide web-based application dedicated to the management of omics data (e.g. Next Generation Sequencing) produced by the different EMBL research groups. EmBASE uses a client-server architecture using Django with REST API on the server side and a javascript-based GUI based on React-redux technologies. Additional command line UI implemented in Java are developed for advanced users i.e. computational biologists.

The successful applicant will also be involved in maintaining analysis server (CentOS) and installing new tools/scientific libraries.

She/he is also in charge of supporting users on a daily basis, assembling training materials (e.g. writing of wiki-based documentation/how-to) and organizing tutorials.

Qualifications and Experience

  • Applicants should have an appropriate university degree in computer science or bioinformatics with 3+ years of relevant experience.
  • Extensive experience in web application development/deployment with Python/Django (with REST API) and modern web technologies (e.g. Node.js, HTML5/CSS, ReactJS, AngularJS) is a must.
  • Experience in unix server administration, database administration/design and PHP programming are highly desirable.
  • Java programming, unix shell scripting, experience with high performance computing (on clusters), data analysis knowledge with e.g. R/Bioconductor are advantageous.
  • Additional experience with large dataset management and knowledge of bioinformatics would make you the ideal candidate.
  • The successful applicant will have demonstrated experience using standard software development tools (SCMs, unit/db testing, design patterns, database design, code versioning systems, agile development notions).
  • She/he will be well organized, open-minded, able to work on different projects in parallel, proactive (problem solving skills are essential) and have a user-oriented spirit.
  • The candidate should be able to work independently and also interact well within a team environment.
  • A working knowledge of English is a must.

What we offer

The chance to work with leading, cutting edge technologies both in IT and computational biology
The opportunity to broaden your skills using open source technologies within a bioinformatics context
Development of professional and personal skills
The chance to work in one of the highest ranked scientific research organizations in the world and contribute to this joint effort.
Working in a young and international environment
An initial fixed-term contract of 3 years, renewal up to 9 years
Competitive salaries exempt from national taxes, with additional allowances for families and non-residents
Assistance for relocation if needed

Should you have further questions, please contact charles.girardot@embl.de.

Europe PMC Community Manager (March 2016)

  • Location : EMBL-EBI, Hinxton near Cambridge, UK
  • Category : Staff Member
  • Contract Duration : 3 years
  • Grading : 5 or 6, depending on experience and qualifications
  • Closing Date : 17 April 2016

Job Description : We are looking to recruit a Community Manager for Europe PMC. This new role will reside within the Literature Services team at the European Bioinformatics Institute (EMBL-EBI).

Europe PMC is Europe's largest repository of freely available life sciences research articles, containing over 30 million biomedical research full text articles and abstracts. These records are supplemented with links to biological databases, citation networks, and text-mined annotations. We run a highly accessed web site, and also offer Europe PMC as a platform for application developers and text miners. Europe PMC is supported by 27 funders of biological and biomedical research across Europe, led by the Wellcome Trust, and is the primary repository for the research article outcomes of the research they fund.

As the Europe PMC Community Manager, your mission is to engage our diverse stakeholder communities around Europe PMC services and build relationships with related service providers. We expect the appointed Community Manager to bring demonstrable experience in most of the key skill areas we require, from a highly related domain such as life sciences research or scientific journal publishing. We think it is critical that you have insight into our core user communities and the roles in which they use Europe PMC from direct experience in the field. You will be computer/technology literate and have a good working knowledge of the web-based tools and platforms that support effective community management.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.

Qualifications and Experience

As the first Community Manager for Europe PMC, you will need to develop a strategic approach to managing and communicating with key stakeholder groups such as researchers, programmatic users, funders and related service providers. To do this you will have the support of the team leader, user experience, author support and technical staff. Alongside building key stakeholder communities, a critical part of the Europe PMC Community Manager's job will be to spot trends and communicate emerging requirements from those groups back to the team. As such you will contribute to the development of the Europe PMC roadmap and build communication channels back to those communities on roadmap milestones. Data collection and analysis skills will help demonstrate the impact of your activities to the team leader and the Europe PMC governance structures.

In addition to strategic skills, we are looking for a Community Manager with strength in the area of engagement. One of the key challenges we need to address for Europe PMC is behaviour change, and how to recruit and retain new users. Content writing and communication skills are also critical: you should be able to write/edit, plan events (such as workshops and hackathons), and write communication plans. You should be prepared to contribute to website content, articles, give presentations and webinars, and lead on social media and blog channels.

This is a new and undoubtedly challenging position where you will find yourself working on an exciting project in a collegial and dynamic team in an international environment. If you think you can fulfil the role and like the idea of operating in the "big data" context of EMBL-EBI, then we would like to hear from you.

Additional Information

The position is full-time, although we will consider applications from people wishing to work part-time on a job-sharing basis. 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.

The initial contract is for a period of 3 years with the possibility of a fixed-term extension.

Application Instructions

Along with your CV, please supply a short statement (less than 1000 words) on how you would approach fulfilling the needs of the position. If you are selected for interview, we will ask you to prepare a brief presentation on this theme.

Web Developer (February 2016)

  • Location : Heidelberg, Germany
  • Category : Staff Member
  • Contract Duration : 3 years
  • Grading : 6, 7 or 8, depending on experience and qualifications
  • Closing Date : 24 April 2016

Job Description : The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

The IT Services department is seeking a highly motivated Web Developer. Together with the team s/he will be responsible for developing the enterprise software infrastructure supporting EMBL's users communities.

Your Qualifications and Experience

Degree in Computer Science or a related subject area
General knowledge of current web technologies including HTML5, JS, PHP, Java..
Familiar with relevant database technologies such as MYSQL, Oracle, Postgress…

Nice to have

Previous exposure to SAP integration
Application server management (Tomcat, Glassfish, …)
Linux system management
Corporate identity and access management (LDAP, SSO, SAML,…)

What we offer

The chance to work with leading, cutting edge technologies
The opportunity to broaden your skills using commercial and open source technologies within an enterprise context
Continued certified training and development of professional and personal skills
The chance to work in one of the highest ranked scientific research organizations in the world and contribute to this joint effort.
Competitive salary & benefits
Working in a young and international environment
Assistance for relocation if needed

Scientific Curation Trainee (February 2016)

  • Location : EMBL-EBI - Hinxton near Cambridge, UK
  • Category : Trainee
  • Contract Duration : 6 months
  • Grading : Training Allowance - There is a small training allowance available, up to £800 a month for full-time trainees (pro-rated for part-time). You will be mentored and given opportunities to expand your skill set and enrich your CV.
  • Closing Date : 06 March 2016 - Interviews will take place in the week of 14 March 2016.

Job Description : A trainee position is available to join the NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) within the Vertebrate Genomics team at the European Bioinformatics Institute (EBI). This trainee position will offer the opportunity to learn about, and gain practical experience in the extraction of detailed scientific information from published scientific papers into the GWAS Catalog and the further development of this widely used resource.

The intern will work within a team of Scientific Curators at the EBI and in collaboration with scientists at the National Human Genome Research Institute (NHGRI).

Qualifications and Experience

Applicants should have an undergraduate degree in genetics or biological sciences. (S)he should have an in-depth understanding of genetic variation and genomics. Experience or knowledge of genome wide association studies and data curation would be advantageous.

The post holder must show strong self motivation to work both independently and as part of a closely interacting team of international scientists. Skill in delivering a high quality product with attention to detail and within fixed deadlines is necessary.

Excellent communication and interpersonal skills are essential.

Objectives

Extraction of information from published scientific papers for inclusion in the GWAS Catalog.
Working collaboratively as part of an International team of scientists.
Investigation of methods to increase curation efficiency.
Working with EBI staff from other disciplines to improve data extraction, management and access.
Communicating with authors of GWAS studies.

1. Welter,D., MacArthur,J., Morales,J, Burdett,T., Hall,P., Junkins,H., Klemm,A., Flicek,P., Manolio,T., Hindorff,L. and Parkinson,H. (2013 ) The NHGRI GWAS Catalog, a curated resource of SNP-Trait associations. Nucleic Acids Research, in press.

2. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America, 106, 9362–7.

  • The EBI, part of the European Molecular Biology Laboratory (EMBL), is a world-leading bioinformatics centre providing biological data to the scientific community, with expertise in data storage, analysis and representation.
  • The Vertebrate Genomics Team at the EBI includes Ensembl, the European Genome-phenome Archive (EGA) and 1000 Genomes data coordination centre. This environment provides access to an international collection of projects at the cutting edge of human variation research. We provide a dynamic, international working environment and have close ties with the University of Cambridge and the Wellcome Trust Sanger Institute.
  • EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.

Postdoctoral Fellow - Heidelberg Human Bioinformatics (HD-HuB) (January 2016)

  • Location : Heidelberg, Germany
  • Category : Postdoctoral Fellow
  • Contract Duration : 3 years
  • Grading : N/A
  • Closing Date : 31 March 2016

Job Description : The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

We are seeking a Bioinformatician to join the Zeller team in the area of metagenomics and human multi-omics data analysis, integration and interpretation. You will develop new analytical methods, implement robust software and integrate tools into workflows and service portals. The position is embedded in the context of the German National Bioinformatics Infrastructure Network (de.NBI), of which the Heidelberg Human Bioinformatics (HD-HuB) node is committed to providing human-centered bioinformatics tools and services.

Your experience acquired while working with these tools will be the basis for delivering insightful, high-quality data analyses, showcasing the potential of these tools in a range of different research projects. For this you will have the opportunity to work closely with other scientists from Georg Zeller's, Peer Bork's, Wolfgang Huber's, Jan Korbel's and / or Toby Gibson's groups.

Additionally, you will interact with, and ideally participate in, internal bioinformatics community initiatives at EMBL (e.g. the Bio-IT project) and explore synergies with external de.NBI / HD-HuB support.

Qualifications and Experience

Requirements for this position include: a PhD degree, preferably with a technical, methods-oriented focus and with exposure to biological research. Programming skills (knowledge of R and / or Python are most valuable) and familiarity with Unix / Bash are essential.

The ideal candidate will additionally have experience with some of the following: developing and maintaining bioinformatics tools; deploying software, e.g. as a web service, Galaxy pipeline or virtual machine; and / or knowledge of HTML and web development. Expertise in analyzing microbiome or other high-throughput genomic data is a plus. Good communication and organisational skills including written and spoken English are required (German language proficiency is not essential). A desire and ability to work well within a team are key to success in this environment.

Additional Information

For more information, please (informally) contact Georg Zeller zeller@embl.de.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

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