Bioinformatics.org
[OMICtools]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (41147+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • Career Center - News

    Featured announcements

    Submit a job announcement | Summary view of positions by date | Subscribe or unsubscribe

    Latest announcements
    Submit Archive Subscribe

    BACKGROUND

    The Computational Biology and Bioinformatics group (3BIO-BioInfo) of the Brussels University (ULB) is seeking candidates for a postdoctoral position.

    Research context:
    Maintaining the stability and interactions of structured proteins is a necessary condition for them to function properly. Designing variants with optimized stability or affinity is a way to create new functional proteins that are stable in various conditions, even outside their physiological range. On the other hand, interpreting the molecular effect of genetic variants is a fundamental step in understanding the pathogenesis processes and a prerequisite to set up personalized drugs and therapies.

    Considering that experimental techniques are slow and costly, the challenging development of efficient bioinformatics tools, capable of predicting the change in protein stability and interactions upon mutations, could guide and limit the experiments that must be performed to identify relevant mutants. Such tools, usually based on combinations of physics-based and machine-learning approaches, possess a large series of applications in the biotechnological sectors from food to biofuel industry, as well as in the biomedical sector focused on genetic diseases. They also present a fundamental interest as they shed some light on the relationship between protein sequence, structure and function, a longstanding problem in protein science, as well as on the genotype-phenotype relationship.

    Furthermore, understanding how natural evolution guided protein mutations and led from ancient to current proteins, and what exactly drives this evolution, is another motivating issue. Although stability and natural evolution are obviously linked, their exact relation is complex and far from known.

    RESPONSIBILITIES

    Objective: Design, develop and apply dedicated software for predicting and gaining understanding of protein stability and interactions, of disease-causing variants, and/or of evolutionary pressure.

    REQUIREMENTS

    Required:
    • PhD degree in Sciences (Bioinformatics, Bioengineer, Physics, Chemistry, Informatics)
    • Excellent programming and computer science skills
    • Excellent communication skills in English
    • Excellent publication record

    PREFERENCES

    Desirable:
    • Experience in the area of protein structural bioinformatics, physics-based approaches and machine learning

    COMPENSATION

    Offer: A full time postdoctoral position for 12 months starting between September and December 2019, financed by the FNRS Fund for Scientific Research, with the possibility of extension through an FNRS postdoctoral research grant or a Marie Curie EC grant.

    HOW TO APPLY

    Please submit to Marianne Rooman (mrooman[at]ulb.ac.be): (1) a cover letter detailing your background and interest in the position, (2) a full CV and (3) two references (with name, email, address, phone number).

    DEADLINE

    Please submit your application by September 15, 2019.

    Submitter

    BACKGROUND

    A world leader in innovative approaches to drug discovery, and global pharmaceutical company based in Cambridge is currently recruiting for an experience Data Scientist to join their thriving bioinformatics team. This role would be responsible for providing expert statistical guidance to support across multi-disciplinary teams throughout the drug discovery, pre-clinical and clinical pipeline.

    The ideal candidate would be highly technical with expertise in either mathematical modelling, predictive analytics or machine learning as applied to complex biological data sets.

    This is a fantastic opportunity for a talented Bioinformatics Data Scientist/Mathematical Modeller who loves the challenge of developing innovative approaches to analyse complex, multi-layered biological data. This company is making huge advancements in the field of cancer and neurology, and this position would have a huge impact on the lives of real patients.

    RESPONSIBILITIES

    Primary responsibilities may include:
    • Developing and implementing novel analytic approaches to analyse diverse multi-layered omics data to identify novel drug targets and biomarkers
    • Develop predictive models using mathematical, machine learning, AI or statistical approaches for biomarker development and patient stratification.
    • Integration and meta-analysis of public and proprietary data sets to generate testable hypothesis

    REQUIREMENTS

    The ideal candidate will have:
    • A PhD or MSc in a numerate discipline eg, Mathematical Biology, Mathematics, Physics, Data Science, Statistics, Machine Learning etc.
    • Demonstrable knowledge of a range of statistical techniques eg, Bayesian Statistics, Probabilistic Programming and graphical models
    • Strong knowledge of a variety of machine learning methods
    • Strong coding skills, proficient in R or Python
    • Previous experience working with complex biological or 'omic's datasets, eg. Proteomics, Genomics, Transcriptomics
    • Previous experience of identifying targets or biomarkers from genomics data would be advantageous, but not an essential requirement!
    • Friendly, approachable nature, and someone that enjoys a sociable, team environment!

    HOW TO APPLY

    For more info, send your CV to efrancis[at]pararecruit.com, or call Emilie for an informal chat on 0121 616 3477.

    Key words: Oncology, Cancer, Tumour, Genomics, NGS, Bioinformatics, Bioinformatician, Mathematical Modeller, Systems Biology, Machine Learning, Drug Targets, AI, Data Scientist, Cambridge, Biotech, Pharma

    Submitter

    BACKGROUND

    The Department of Medical Microbiology and Infectious Diseases in the Rady Faculty of Health Sciences, University of Manitoba, in conjunction with Canada's National Microbiology Laboratory (NML), invites applications for a Post-Doctoral Research Associate position for up to three years in the Van Domselaar Lab for Bioinformatics. The project will focus on the development of Proksee, expert system for bacterial genome assembly, annotation, visualization, and analysis.

    For more information: www.genomecanada.ca/en/c[...]depth

    REQUIREMENTS

    Applicants must have a Ph.D. in Bioinformatics, Genomics, Computer Science, or a closely related field at the time of hiring. Strong programming skills are essential. Practical experience with next-generation sequencing data analysis, statistics, and solid knowledge of microbial genomics is highly desirable.

    PREFERENCES

    Preference will be given to self-motivated candidates with evidence of publications, excellent communication skills, an ability to work well in a team environment, and strong interest in software engineering.

    ABOUT US

    The NML represents Canada's main infectious disease public health lab with responsibility for reference lab-based surveillance for infectious diseases, emergency outbreak preparedness and response, training, and research and development. The NML is Canada's only Level 4 Biosafety Laboratory in Canada, and only one of a handful around the world. In modernizing Canada's surveillance and response framework, the NML has and made heavy commitments to transition Canada's public health system to incorporate genomics technologies across all of its science programs. These investments include over $10 million in high performance computing, and nearly two dozen high throughput sequencing instruments, including short-read and long-read technologies, making it one of the largest generators of microbial genomics data in the world. The Van Domselaar Lab for Bioinformatics at the NML is regarded as one of the top public health bioinformatics labs in the world.

    HOW TO APPLY

    To apply, please submit a CV, a research statement describing accomplishments and current interests, and a list of three references to gary.vandomselaar[at]canada.ca.

    DEADLINE

    Review of applications will begin on August 1, 2019 and continue until the position is filled.

    POLICY

    Successful applicants must be eligible to obtain a Canadian Secret (Level II) security clearance. Thus, preference is given to Canadian citizens / permanent residents having resided in Canada for over ten years and have no criminal convictions.

    Submitter

    BACKGROUND

    To build on the success of the 100,000 Genomes Project, the Government tasked NHS England with support from Genomics England to launch a new NHS Genomic Medicine Service comprising a National Genomic Test Directory where 300,000 tests have been re-profiled and whole genome sequencing will be available for direct healthcare. Through 7 Genomic Laboratory Hubs this offers equitable access to the 55 million people in England to the latest genomic medicine and research. This will lead to faster diagnosis and personalised medicine.

    Genomics England has been asked to prepare a plan for up to 5 million genomic tests over the next 5 years.

    The post holder provides high calibre bioinformatics research support to external researchers and industrial partners by enabling analysis, facilitating access to datasets and ensuring optimal use of the Genomics England Research Data Centre. The post holder will act as a second line of support for users of the Research Environment. They will be intimately familiar with the data and applications.

    The research support team is also tasked with quality assuring the data and applications released into the research environment. The role includes elements of a bioinformatician and data analyst, ensuring that our users have an excellent customer experience.

    RESPONSIBILITIES

    Key Accountabilities:
    • Understanding Genomics England datasets and the research environment, and being both a super user and advocate internally and externally
    • Understanding the needs of customers (academic, NHS and industry); working with customers to ensure that their scientific projects are successful
    • Carrying out custom analyses on demand
    • Managing data; supporting data generation, intake, and extraction through airlocks
    • Supporting users with how to use our software and data
    • Keeping track of customer relationships and being the internal authority on specific customer issues, needs, and future plans
    • Providing high calibre troubleshooting of problems for customers, appraise customers and Genomics England options and execute solutions, co-ordinating with internal teams when necessary
    • Contributing to the development of the Research Environment through identifying unmet customer needs, suggesting solutions, and improving supporting material
    • Collaborating internally, particularly with others in the Chief Scientist's team, our Commercial team, Bioinformatics team and platform engineers, to develop and deploy suitable solutions for customers
    • Working from time to time on the NHS Clinical Interpretation pipeline

    REQUIREMENTS

    Key Requirements:
    • Extensive experience in analysis of large-scale genomic data using bioinformatics tools and pipelines
    • Demonstrable experience in using next generation sequencing data
    • Competence in R, Python or similar language appropriate for large-scale genomics analysis
    • Strong communication skills, both written and verbal and excellent facilitation, influencing and presentation skills
    • Good customer-service orientation, disposition to help, and experience in working with customers, preferably in the scientific/pharma industry
    • Excellent team working skills and comfortable working as part of matrix teams and as part of external teams to ensure delivery
    • Experience with high-performance computing or cloud-scale data processing
    • Adaptable to an ever-evolving working environment
    • Background in human disease genetics, preferably in cancer or rare disease, demonstrated by publication record or industry track record
    • Educated to MSc level (or higher), in Bioinformatics, Biostatistics, Statistical Genetics, or a related scientific discipline
    • Proven ability to communicate with stakeholders from diverse backgrounds (e.g. management, IT, R and D, biology, bioinformatics)
    • Willingness to travel occasionally (<15%) to meet customers or to attend events to gain market insight
    • Experience of working in a knowledge sharing environment
    • Proven understanding of clinical and phenotypic data management and the sensitivities surrounding patient cohort data

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Support, Bioinformatics, Research, NGS, Matrix, HPC, Statistical, External, QA, Analysis, Cohort, Cloud, Human, Genetics, Cancer, Rare, Disease, London

    BACKGROUND

    GDIT supports the world's largest supercomputer dedicated to life sciences and biomedical research. In the past two years we've delivered 14X growth in compute and 5X in storage for NIH. We are looking to expand our NIH onsite HPC support with individuals who can also contribute to GDIT's HPC Center of Excellence across programs in NASA, NOAA, Defense and Intelligence communities.

    RESPONSIBILITIES

    We are looking for an experienced individual with a strong Linux background, configuration management, systems automation and network monitoring to join our team to administer the NIH Biowulf supercomputer. The position is full-time onsite at the NIH main campus in Bethesda, Maryland.

    This position supports the HPC systems administrative team in operating and maintaining the 3,000 node Linux cluster for ~2,000 biomedical researchers.

    Specific responsibilities include:
    • Work with systems staff to enhance configuration management infrastructure.
    • Evaluate performance impacts of planned operating system changes.
    • Update and expand existing systems monitoring capabilities.
    • Develop automation tools for cluster administration.
    • Participate in resource optimization and job scheduling software and policies.
    • Provide technical support to researchers using HPC resources, troubleshoot problems and develop appropriate computational strategies.
    • Consult and collaborate with scientist coworkers to determine best system configurations for applications.

    REQUIREMENTS

    • BS degree and 8+ years of related experience; or a MS and 6+ years of related experience or the equivalent combination of experience/education
    • Minimum of eight years RedHat or CentOS Linux system administrator experience in an HPC environment
    • Minimum of 9+ years programming experience in at least two languages: C/C++, Python and Perl
    • Prior experience with configuration management tools, such as Ansible, Chef, Puppet, Cobbler
    • Demonstrated ability to configure, deploy and manage a major system area such as batch system, network, data storage, backup system, database system, or distributed computing

    PREFERENCES

    • Experience with batch systems such as SLURM or PBS
    • Experience managing parallel and cluster file systems such as NFS, GPFS, or Lustre
    • Network management experience especially Infiniband
    • Experience integrating applications with cloud provider software stack
    • Experience presenting and/or teaching
    Attributes for success:
    • Provide leadership and technical expertise to improve HPC cluster performance and resiliency
    • Ability to work both independently and as part of the team; flexibility in dealing with assignments and in working on several projects simultaneously
    • Ability to effectively communicate with people of diverse backgrounds and computer knowledge

    TERMS

    • The position is full-time onsite at the NIH main campus in Bethesda, Maryland.
    • Limited off-hour system maintenance activities will be planned in advance.
    • There are no travel requirements.
    • Applicants must be US citizen or permanent resident to meet moderate level security requirement of facility.

    LOCALE

    Bethesda, MD

    HOW TO APPLY

    Please visit csra.wd5.myworkdayjobs.com/Exte[...]213-1

    BACKGROUND

    About the Job:
    The Institute for Health Informatics at the University of Minnesota invites applications for multiple Postdoctoral Associate positions from candidates with a Ph.D or equivalent degree in bioinformatics or related disciplines. The translational genomics and bioinformatics group directed by Dr. Steven S. Shen, M.D., Ph.D., is seeking outstanding scientists who are interested in working in a research program studying the genome wide mapping of epigenetic elements and the mechanism of gene expression regulation in mammals.

    The ideal candidate should have experience in bioinformatics and computer programming, especially NGS data analysis. Familiarity with public DNA/RNA sequencing data repository will be needed to study the distribution of genome-wide epigenetic elements and the correlation with gene expression control. The candidate must have the ability to define research questions and develop experiment designs to address those questions. The candidate should have experience presenting research results through publications and presentations.

    About the Department:
    The Institute for Health Informatics at the University of Minnesota is a well-balanced program with significant achievements in teaching, clinical programs and research. The University of Minnesota is one of the highest ranked public universities in research. The successful applicant will receive training in, and be expected to participate in the design, implementation and evaluation of experiments related to on-going NIH funded research. The University of Minnesota shall provide equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression.

    RESPONSIBILITIES

    • Develop research questions based on genome-wide distribution of epigenetic elements and the control mechanism of gene expression (20%)
    • Collect data (20%)
    • Analyze data (30%)
    • Write manuscripts for publications (15%)
    • Collaborative research projects (15%)

    REQUIREMENTS

    Minimum qualifications:
    • PhD in bioinformatics, computer science, mathematics, or related science field
    • Expertise in DNA/protein sequencing data, NGS data, genomics and epigenetic data analysis,
    • Excellent interpersonal skills and ability to work collaboratively with others.
    • Excellent oral and written communication skills
    Preferred qualifications:
    • Experience working gene expression profiling, DNA and histone methylation
    • Experience in genome wide DNA and histone marker discovery
    • Experience in machine learning technology
    • Experience statistical analysis of experimental data
    • Record of presenting research results through publications and conference abstracts

    HOW TO APPLY

    Applications must be submitted online (hr.myu.umn.edu/jobs/ext/326907), or search for Job ID # 326907 (hr.myu.umn.edu/psc/[...]eId=1). To be considered for this position, please click the Apply button and follow the instructions. You will be given the opportunity to complete an online application for the position and attach a cover letter and resume.

    Additional documents may be attached after application by accessing your "My Activities" page and uploading documents there.

    To request an accommodation during the application process, please e-mail madso009 at umn (dot) edu or employ at umn (dot) edu or call (612) 624-UOHR (8647).

    COMPENSATION

    $50K – 65K (commensurate with experience)

    POLICY

    Diversity:
    The University recognizes and values the importance of diversity and inclusion in enriching the employment experience of its employees and in supporting the academic mission. The University is committed to attracting and retaining employees with varying identities and backgrounds.

    The University of Minnesota provides equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression. To learn more about diversity at the U: diversity.umn.edu.

    Background Check Information:
    Any offer of employment is contingent upon the successful completion of a background check. Our presumption is that prospective employees are eligible to work here. Criminal convictions do not automatically disqualify finalists from employment.

    BACKGROUND

    Inivata is a leader in liquid biopsy. Our InVision® platform unlocks essential genomic information from a simple blood test to transform the care of cancer patients. Our technology is based on pioneering research from the Cancer Research UK Cambridge Institute, University of Cambridge and backed by multiple high calibre publications. Our lead product, InVisionFirst™-Lung, is commercially available and provides molecular insights that enable clinicians to make more informed treatment decisions for NSCLC patients. Inivata is actively partnering with pharmaceutical and biotechnology companies on InVisionFirst™-Lung and our wider platform, which is applicable to a range of cancer types. We have a CLIA laboratory in Research Triangle Park, NC and laboratories in Cambridge, UK.

    The R&D Computational Biology group are looking to recruit a highly motivated, creative and logical individual with strong bioinformatics and computational skills. This role will be placed within the newly formed pipeline team which oversees the development and maintenance of the company's production pipelines. The candidate will work closely with the bioinformatics, software development and system administration teams to develop new pipelines into robust and scalable products. The candidate will have strong communication skills, a delivery focused attitude and the ability to interface with different teams. This position offers the exciting opportunity to work at the frontier of liquid biopsy-based cancer diagnostics, seeking entire product development pipeline from concept, clinical validation, to commercial product.

    This role will involve applying a deep understanding of HPC to the analysis of NGS cancer genomics variant data and innovative algorithm design. We expect that applicants will have prior experience in the field of bioinformatics and a solid background in pipeline development and optimisation in relation to NGS analysis; for example, an MSc or PhD degree in a relevant field and/or industry experience.

    There is flexibility for the exact profile and experience of the applicant, provided that they can demonstrate qualities in the general area of computational Biology and the motivation to join a rapidly growing company in the field of cancer genomics.

    RESPONSIBILITIES

    • Develop new and scale existing algorithms and pipelines to production ready, regulatory compliant cancer diagnostics products.
    • Interface between bioinformatic, software development and system administration teams to prioritise and organise work.
    • Contribute to quality management of computational biology processes and development of systems that conform to regulatory standards.

    REQUIREMENTS

    • PhD in the field of computational biology/bioinformatics, or significant experience in that space
    • Proven track record with HPC in context of biomedical data analysis (essential)
    • Experience with implementation and maintenance of NGS data analysis pipelines (essential)
    • Full working proficiency in Python and R (essential)
    • Full working proficiency in Linux system administration (essential)
    • Full working proficiency in relational databases, such as MySQL, PostgreSQL or Oracle (essential)
    • Full working proficiency in software versioning systems, eg. git, svn (essential)
    • Knowledge of cancer genomics (desired)
    • Full working proficiency in a compiled language, preferably C or C++ (desired)
    • Experience with algorithm and systems design for parallel computing (desired)
    • Experience with Docker (desired)
    • Experience with AWS products, including EC2, Batch, S3, Lambda (desired)
    • Prior experience with work in a regulated environment, in particular for software and quality assurance, such as ISO 13485, EN 62304, ISO 15189, or other (desired)

    LOCALE

    Inivata Limited is based in Cambridge, UK.

    HOW TO APPLY

    Please apply using this link: cezanneondemand.intervieweb.it/iniv[...]1/en/

    No agencies please.

    www.inivata.com

    Submitter

    BACKGROUND

    This is a great role for a data science expert to join a world leading cancer analysis team based in Cambridge focused on understanding the role of genetics in health and disease. The organisations' mission is to use genome sequences to advance understanding of human and pathogen biology in order to improve human health.

    A successful applicant will help making sense of huge and complex data, inferring relationships between variables, identifying those variants which act as drivers of disease, and then correlating how they work together to cause disease progression.

    REQUIREMENTS

    Essential Skills Include:
    • PhD in Computer Science discipline or equivalent experience
    • Self-motivated, able to work independently and organise own workload
    • Demonstrated ability to independently run data science project
    • Excellent communication and effective team-working skills
    • Working knowledge of at least one programming language

    PREFERENCES

    Ideal Skills Include:
    • Experience of scientific software development
    • Familiarity with machine learning methods
    • Knowledge of human or cancer genetics

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Cancer, Data, Scientist, Bioinformatics, Genomics, Python, C++, Machine Learning, Keras, TensorFlow, Human, Genetic, Statistics, Analysis, HPC, Cambridge

    BACKGROUND

    EchinoBase is hiring a Biocurator to work within the laboratory of Charles Ettensohn in the Department of Biological Sciences at Carnegie Mellon University. EchinoBase is an online platform that houses genomic and transcriptomic resources of echinoderms. The mission of EchinoBase is to serve as a central database for an international community of researchers interested in understanding echinoderm biology from a genomic perspective. In this aim, EchinoBase maintains information on the organization, function and evolution of echinoderm genes. Two active research labs in the department use echinoderms as model systems. This provides an excellent opportunity to interface first-hand with members of the community. As an NIH-funded community resource, EchinoBase provides a supportive environment with many training opportunities available.

    The Mellon College of Science (MCS) is home to four departments and many programs and research centers that cross disciplines. We approach scientific problems from fresh angles using creative interdisciplinary approaches while drawing on our departmental strengths in the core sciences. MCS faculty members are nationally and internationally recognized for their research in a variety of fields, including polymer science, cosmology, mathematical finance and neuroscience.

    RESPONSIBILITIES

    • Curate existing and new literature on echinoderm biology and highlight this literature on Echinobase.
    • Evaluate primary literature for data on spatiotemporal gene expression patterns in echinoderms.
    • Annotate gene expression patterns using standardized anatomical and genetic vocabularies
    • Integrate published information on echinoderm genes into the existing database.
    • Interface with existing Echinobase database structure and software.
    • Communicate with journals and publishers for copyright permissions.
    • Build trusted relationships with an international community of echinoderm researchers, including providing feedback to researchers.
    • Generate and contribute content to Echinobase, including FAQ pages, tutorials and publications.

    REQUIREMENTS

    • Knowledge of echinoderm biology and development. A Bachelor's degree in life sciences is required, although a MSc or PhD is preferred.
    • Excellent verbal and written communication skills
    • Familiarity with literature databases such as Pubmed and Google Scholar
    • Ability to read and analyze scientific literature, including experimental details and data limitations
    • Self-motivated, detail-oriented problem solver with the ability to prioritize work
    • Computer skills, including word processing and spreadsheet applications

    HOW TO APPLY

    See cmu.taleo.net/care[...]12868 for more details and application instructions.

    BACKGROUND

    The Mellon College of Science (MCS) is home to four departments and many programs and research centers that cross disciplines. We approach scientific problems from fresh angles using creative interdisciplinary approaches while drawing on our departmental strengths in the core sciences. MCS faculty members are nationally and internationally recognized for their research in a variety of fields, including polymer science, cosmology, mathematical finance and neuroscience.

    EchinoBase is hiring a Bioinformatician to work in the lab of Veronica Hinman in the Department of Biological Sciences at Carnegie Mellon University (Pittsburgh, PA). EchinoBaseis an online platform that houses genomic and transcriptomic resources of echinoderms. The mission of EchinoBase is to serve as a central database for an international community of researchers interested in understanding echinoderm biology from a genomic perspective. In this aim, EchinoBase maintains information on the organization, function and evolution of echinoderm genes. In this role, you will work alongside other EchinoBase personnel.

    The Department of Biological Sciences at CMU is the physical home of EchinoBase. Two active research labs in the department use echinoderms as model systems. This provides an excellent opportunity to interface firsthand with members of the community. As an NIH-funded community resource, EchinoBase provides an encouraging environment with many training opportunities available.

    RESPONSIBILITIES

    • Assembling and annotating echinoderm genomes
    • Establishing and maintaining high-quality pipelines for analyzing genomic and transcriptomic datasets
    • Developing web-based data viewers
    • Generating and contributing content to EchinoBase, including FAQ pages, tutorials and publications

    REQUIREMENTS

    • MSc. or a Ph.D. is desirable in life sciences or related field.
    • Experience with bioinformatic data analysis
    • Familiarity with genomics and molecular biology
    • Ambitious, problem solver with the ability to prioritize work
    • Outstanding attention to detail and strong analytical skills
    • Excellent verbal and written communication skills

    HOW TO APPLY

    Are you interested in the position with us? Please apply.

    See cmu.taleo.net/care[...]12984 for more details and application instructions.

    BACKGROUND

    The Joint Genome Institute (JGI) within Berkeley Lab has an exciting career opportunity available for a microbiome researcher with an interest/experience in data pipeline development and portability. The Department of Energy is funding a pilot program, the "National Microbiome Data Collaborative" (NMDC) which aims to address many of the pressing issues in microbiome research, including data integration, making data FAIR (findable, accessible, interoperable, and reusable) and establishing standardized workflows for data processing.

    In this role the NMDC software engineer will work closely with JGI's IMG group and collaborate with a diverse set of engineers and scientists, to port and standardize IMG's annotation pipelines through a workflow language (e.g. CWL) and incorporate them into standalone software packages (e.g. Docker containers) that can be freely obtained and run in any environment.

    This position is within the IMG Pipelines Group and will report to the IMG Pipelines Group team lead at the Joint Genome Institute in Berkeley, CA.

    Classification will depend upon the applicant's level of skills, knowledge, and abilities. This position will be filled at the Computer Systems Engineer 2 or Computer Systems Engineer 3 level, dependent on experience.

    RESPONSIBILITIES

    What You Will Do (Computer Systems Engineer – Level 2):
    • Work on porting and standardizing portable and scalable data pipelines.
    • Ensure accurate software version control, testing and release engineering.
    • Create documentation and training materials.
    • Serve as a key contributor called upon to troubleshoot and recommend solutions to technical problems.
    Additional Responsibilities as needed (Computer Systems Engineer – Level 2):
    • Present to audiences within and outside the lab.
    • Assist with the curation and processing of legacy and current data and metadata.
    In addition to the above, the Computer Systems Engineer 3 responsibilities include:
    • Work on complex issues where analysis of situations or data requires an in-depth evaluation of variable factors. Exercise judgment in selecting methods and techniques to improve genomic analysis within the IMG Pipelines.
    • Take a lead role in analyzing and evaluating varied factors in produced predictions, perform manual curation and large-scale computational analysis of predicted gene models and annotations.
    • Take a lead role in developing processes/procedures and providing and improving protocols, methods and tools for genome annotation and analysis.
    • Lead the efforts to proactively look for additional opportunities to make contributions to the IMG Pipelines.
    • Networks with key contacts outside of JGI.

    REQUIREMENTS

    Minimum Qualifications for Computer Systems Engineer – Level 2:
    • Bachelor's degree in Computer Science, Engineering, Bioinformatics, or a related field with a minimum of 5 years of work experience, or an equivalent combination of education and experience.
    • Demonstrated experience with the entire software development process, from requirements through design to implementation and deployment.
    • Proficiency programming in Python.
    • Experience in creating workflows via a workflow language.
    • Experience in the containerization of applications (e.g. via Docker).
    • Experience with CI/CD tools and frameworks (e.g., Gitlab, Jenkins).
    • Experience with modern cluster/cloud/distributed computational and storage systems.
    • Experience applying modern software technologies for databases, RESTful services, computational workflows, data processing pipelines, and/or scientific reproducibility.
    • Working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
    • Familiarity with SQL and relational databases such as Oracle, MySQL or Postgres.
    • Ability to conduct analysis and work independently.
    • Excellent English written and oral communication.
    • Strong interpersonal skills for working in a diverse team environment.
    In addition to the above, the Computer Systems Engineer 3 qualifications include:
    • Minimum of 8 years of related experience with a Bachelor's degree; or 6 years and a Master's degree; or equivalent experience.
    • Excellent track record of success in previous employment.
    Additional desired qualifications for Computer Systems Engineer – Level 2:
    • Master's degree or equivalent work experience.
    • Demonstrated experience working in similar fields.
    • Familiarity with different types of sequence data.
    • Demonstrated experience working in high-performance computing.
    Desired qualifications for the Computer Systems Engineer 3:
    • Experience with genomic analysis software, and knowledge of various bioinformatics algorithms related to sequence analysis.
    • Ability to provide creative and in-depth solutions to pipeline or analysis issues encountered at work.
    • Ability to suggest, design and implement new, useful features to improve the IMG Pipelines.
    • Ability to constantly keeping up with technology changes in the field.

    TERMS

    • This is a full time, 2 year term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
    • Classification will depend upon the applicant's level of skills, knowledge, and abilities. This position will be filled at the Computer Systems Engineer 2 or Computer Systems Engineer 3 level, dependent on experience.
    • Full-time, M-F, exempt (monthly paid) from overtime pay.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

    LOCALE

    Work will be primarily performed at JGI/Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    COMPENSATION

    Salary is commensurate with experience.

    Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding employee development opportunities. To view information about the many rewards that are offered at Berkeley Lab- Click Here (commons.lbl.gov/display/hr/Benefits).

    ABOUT US

    JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest
    They say it's all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class science within a diverse, respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Institute (JGI) addresses the most pressing energy and environmental challenges. This summer, JGI takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of the next ground-breaking discoveries in the public interest?

    The JGI is comprised of highly-skilled and diverse talent founded on a culture of scientific excellence, trust, curiosity, passion, and collaboration.

    Berkeley Lab (LBNL, www.lbl.gov) addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]64254 and follow the on-line instructions to complete the application process.

    DEADLINE

    The posting shall remain open until the position is filled.

    POLICY

    Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4 (www.dol.gov/ofcc[...].html). Click here (www.dol.gov/ofcc[...]t.pdf) to view the poster: "Equal Employment Opportunity is the Law".

    Submitter

    BACKGROUND

    This is a great opportunity for a LIMS Developer to join a world-leading organisation working in liquid biopsy. The developer will ensure productivity of an automated Clinical Lab and help develop the LIMS platform alongside new laboratory technology.

    RESPONSIBILITIES

    Key Responsibilities:
    • Interfacing between the LIMS users and the Computational team as to establish user requirements
    • Develop User Guides or Work Instruction documents (SOPs)
    • Train and support LIMS users
    • Maintain and create workflows
    • Scripting against the LIMS API
    • Develop IQ, OQ, PQ documentation
    • Conduct UAT testing to ensure that the configuration is meeting the business needs, also resolve any bugs identified during the testing phase
    • Integrating the LIMS with other in house system
    • Supporting the day to day CLIA lab operations by dealing with LIMS issues such as incorrect entries as they arise

    REQUIREMENTS

    Key Requirements:
    • Experience with Python
    • Knowledge of LIMS configuration
    • Experience working with Git repositories
    • Experience with Shell command-line interpreter such as bash
    • Experience with liquid handling robots
    • Understanding of molecular biology and experience with molecular techniques including PCR and NGS
    • Experience with Clarity LIMS,
    • Ability to write review and execute IQ, OQ, PQ documentation
    • Ability to communicate effectively

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: LIMS, Developer, Lab, Informatics, Python, Configuration, Clinical, Genomics, SOP, API, Scripting, CLIA, Git, Bash, NGS, PCR, Workflows, Cambridge.

    Submitter

    BACKGROUND

    This is a great opportunity for a LIMS Lead to join a world-leading organisation working in liquid biopsy. The LIMS Lead supports laboratory operations through the implementation and maintenance of software-based solutions that enhance laboratory workflows, data management, and data sharing. The LIMS Lead works directly with laboratory leadership to define laboratory information technology needs, and assists with the selection of software and supporting hardware to meet those needs. The LIMS Lead works with commercial vendors, information technology (IT) staff, and laboratory staff to implement laboratory IT systems. The LIMS Lead also maintains and enhances laboratory IT systems to meet the constantly changing needs of the laboratory and its clients.

    RESPONSIBILITIES

    Key Responsibilities:
    • Maintain knowledge of IT functions required for LIMS operation including overall system architecture
    • Make decisions that support LIMS selection, implementation, maintenance, and enhancement
    • Lead the RFI and RFP processes, and participate in proposal evaluation and product selection
    • Lead contract negotiation and management
    • Participate in project budgeting and help ensure projects remain within budget
    • Directly manage all projects related to LIMS implementation, maintenance, and enhancement
    • Ensure clear and direct communication with laboratory staff, state IT staff, and vendors throughout LIMS development, testing, implementation, enhancement, and maintenance phases
    • Assist laboratory leadership in defining milestones for the completion of LIMS projects
    • Ensure LIMS requirements are clearly defined and understood by state IT workers and vendors
    • Establish LIMS project priorities through communication with laboratory leadership and vendors
    • Perform LIMS testing and oversee application testing performed by laboratory staff
    • Establish a protocol for error reporting and resolution
    • Establish a protocol for application enhancement and coordinate enhancements with laboratory leadership, laboratory staff, IT staff, and vendors

    REQUIREMENTS

    Key Requirements:
    • Bachelor's Degree in a relevant field or equivalent experience
    • Minimum 5 years' experience in LIMS, python software development
    • 3-5 years management experience in a lead role
    • ** Clarity LIMS experience a plus **
    • In-depth knowledge in laboratory sciences as well as the LIMS and IT needs of a diagnostic lab
    • Deep understanding of lab processes
    • Ability to communicate cross functional
    • Experience with Git or similar version control system

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: LIMS, Laboratory, Informatics, Management, Systems, Leader, Architecture, Implementation, Testing, Software, Hardware, Python, Clarity, Cambridge.

    Submitter

    BACKGROUND

    This is a great opportunity for a strong bioinformatics pipeline developer to join the R&D Computational Biology group who are looking to recruit a highly motivated, creative and logical individual with strong bioinformatics and computational skills.

    This role will be placed within the newly formed pipeline team which oversees the development and maintenance of the company's production pipelines. The candidate will work closely with the bioinformatics, software development and system administration teams to develop new pipelines into robust and scalable products. The candidate will have strong communication skills, a delivery focused attitude and the ability to interface with different teams. This position offers the exciting opportunity to work at the frontier of liquid biopsy-based cancer diagnostics, seeking entire product development pipeline from concept, clinical validation, to commercial product.

    This role will involve applying a deep understanding of HPC to the analysis of NGS cancer genomics variant data and innovative algorithm design. We expect that applicants will have prior experience in the field of bioinformatics and a solid background in pipeline development and optimisation in relation to NGS analysis; for example, an MSc or PhD degree in a relevant field and/or industry experience.

    RESPONSIBILITIES

    Key Responsibilities Include:
    • Develop new and scale existing algorithms and pipelines to production ready, regulatory compliant cancer diagnostics products.
    • Interface between bioinformatics, software development and system administration teams to prioritise and organise work.
    • Contribute to quality management of computational biology processes and development of systems that conform to regulatory standards.

    REQUIREMENTS

    Key Requirements Include:
    • Proven track record with HPC in context of biomedical data analysis (essential)
    • Experience with implementation and maintenance of NGS data analysis pipelines (essential)
    • Full working proficiency in Python and R (essential)
    • Full working proficiency in Linux system administration (essential)
    • Full working proficiency in relational databases, such as MySQL, PostgreSQL or Oracle (essential)
    • Full working proficiency in software versioning systems, eg. git, svn (essential)
    • Knowledge of cancer genomics (desired)
    • Full working proficiency in a compiled language, preferably C or C++ (desired)
    • Experience with algorithm and systems design for parallel computing (desired)
    • Experience with Docker (desired)
    • Experience with AWS products, including EC2, Batch, S3, Lambda (desired)
    • Prior experience with work in a regulated environment, in particular for software and quality assurance, such as ISO 13485, EN 62304, ISO 15189, or other (desired)

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Bioinformatics, Pipeline, Developer, Computational, Biology, Software, Cancer, Diagnostics, Algorithms, NGS, Python, Linux, HPC, Version, Control, SQL, Regulated, Cambridge

    Submitter

    BACKGROUND

    To build on the success of the 100,000 Genomes Project, the Government tasked NHS England with support from Genomics England to launch a new NHS Genomic Medicine Service comprising a National Genomic Test Directory where 300,000 tests have been re-profiled and whole genome sequencing will be available for direct healthcare. Through 7 Genomic Laboratory Hubs this offers equitable access to the 55 million people in England to the latest genomic medicine and research. This will lead to faster diagnosis and personalised medicine.

    The post holder provides high calibre bioinformatics research support to external researchers and industrial partners by enabling analysis, facilitating access to datasets and ensuring optimal use of the Genomics England Research Data Centre. The post holder understands our datasets and how to analyse clinical and genomic data and use tools and services to realise the maximum value from accessing our data.

    There is cross-working with other bioinformatics team members developing our interpretation pipeline for the National Health Service.

    RESPONSIBILITIES

    Your responsibilities will include:
    • Understanding the needs of customers (academic, NHS and industry); working with customers to ensure that their scientific projects are successful and that they gain value from their interactions with our Research Environment. This includes face to face engagement to assess needs and execution.
    • Carrying out complex custom analysis
    • Providing high calibre troubleshooting of problems for customers, appraise customers and Genomics England options and execute solutions, co-ordinating with internal teams when necessary
    • Keeping track of customer relationships and being the internal authority on specific customer issues, needs, and future plans
    • Being the key point of contact with customers collecting and updating requirements, communicating progress and feedback
    • Sharing knowledge within Genomics England about customer needs and experiences and contributing to the development of the Research Environment
    • Collaborating internally, particularly with others in the Chief Scientist's team, our Commercial team, Bioinformatics team and software and infrastructure engineers, to develop and deploy suitable solutions for customers
    • Working from time to time on the NHS Clinical Interpretation pipeline (creating a seamless bioinformatics team who understand the NHS and research pipelines)

    REQUIREMENTS

    You will need to meet the following requirements:
    • A background in a strongly quantitative discipline such as Mathematics, Physics, or Computer Science, ideally with some postdoctoral experience in fields related to statistical genetics or genomics, or a demonstrable equivalent background
    • Strong evidence of experience of bioinformatics research and analytics using large genomic datasets of next generation sequencing data alongside clinical data in a field relevant to Genomics England
    • Strong customer-service orientation and proven expertise in partnership working with customers, preferably in the scientific/pharma industry
    • Excellent communication skills, both written and verbal and excellent facilitation, influencing and presentation skills
    • Proven ability to communicate with key customer and internal stakeholders from diverse backgrounds (e.g. management, IT, R and D, biology, bioinformatics)
    • Excellent team working skills and comfortable working as part of matrix teams and as part of external teams to ensure delivery
    • Experience of working in a knowledge sharing environment
    • Willingness to travel occasionally (<15%) to meet customers or to attend events to gain market insight
    • Strong statistical analysis skills
    • Experience with cloud-scale data processing and high-performance computing
    • Demonstrated knowledge and competence in relevant programming languages and applications (e.g. R, Python) and experience of using a suite of bioinformatics tools to problem solve and answer research questions
    • Ability to work independently with a high degree of motivation and focus, and to complete tasks according to company priorities with minimal supervision
    • Adaptable to an ever-evolving working environment
    • Experience of technical writing
    • Knowledge and competence in relevant applications eg LabKey, OpenCGA
    • Strong publication record in a relevant field, and a proven ability to stay abreast of developments in that field
    • Previous experience of delivering training resources and events
    • Proven understanding of clinical and phenotypic data management and the sensitivities surrounding patient cohort data

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Senior, Analyst, Bioinformatics, Genomics, Statistics, Geneticist, NGS, WGS, GWAS, Population Genetics, London, NHS, Python, HPC, Cloud, Pipelines, NGS, SQL, Matrix, Cohort
    Submit Archive Subscribe

     

    Copyright © 2019 · Scilico, LLC