Bioinformatics Programmer (Research Assistant) in Plankton Genomics Genomics and Regulatory Systems Unit (Luscombe Unit)

The Okinawa Institute of Science and Technology Graduate University (OIST; see www.oist.jp) is a dynamic new graduate university of science and technology in Okinawa Prefecture, Japan. The university is located on 85 hectares of protected forestland overlooking beautiful shoreline and coral reefs. The campus is striking architecturally, and the facilities are outstanding (OIST campus video tour). There are no academic departments, which facilitates multidisciplinary research. Outstanding resources and equipment are provided and managed to encourage easy access and collaboration. English is the official language of the University, and the university research community is fully international, with more than 50 countries represented. OIST is rapidly gaining recognition in the worldwide academic community as a model for excellence in education and research.

Come and join us as a Bioinformatics Programmer!

Are you a talented and motivated recent graduate? We want you to join our lab as a Bioinformatics Programmer to help us analyse the genome sequences of marine zooplankton (https://groups.oist.jp/grsu). You will develop and deploy state-of-the-art computational biology and bioinformatics software to study the populations and evolutionary adaptation of zooplanktons sampled from local and global waters (video).

Fantastic opportunity for a recent graduate

This position is ideal for a recent university or technical school graduate (Diploma, Bachelor’s or Master’s) with programming experience. You will work on primary datasets to ensure accurate and reproducible outputs of all computational analyses performed in our lab. Specifically, you will be trained by senior lab members to become skilled in the Nextflow workflow code, strict version control, test-driven code design, containerisation of execution environments, peer code review, and automated testing and deployment of pipeline releases. The position is a fantastic starting point to a career in science: former Research Assistants from our lab have gone onto prestigious Ph.D. programmes, data science positions in tech companies and some even now lead their own labs at the best institutions in the world.

Who are we?

We are a happy, international and interactive lab: we come together from different countries and diverse academic backgrounds. The lab head, Nick Luscombe, recently joined OIST as a full-time professor. You will be part of an exciting new phase of the lab’s life cycle.

Location 

1919‐1 Tancha, Onna‐son, Okinawa, Japan 904-0495

Responsibilities 

As a Bioinformatics Programmer, you will:

1. deploy software and workflows needed by lab members on OIST’s high-performance computer infrastructure; this includes software updates, source code management, system virtualization, workflow development, testing and operation;
2. develop, extend or implement reproducible computational workflows;
3. process bespoke genomic data alongside publicly available datasets;
4. develop new computational tools for analysing genomic and molecular data;
5. report and present your progress to colleagues at scientific meetings;
6. participate in the writing, submitting and revising scientific papers;
7. keep up with developments in the field and incorporate this knowledge to advance your work;
8. be an effective collaborator and team member;
9. train colleagues in applying your work, as requested by the lab head;
10. carry out routine administrative tasks associated with your work, to ensure it is completed on time and within budget;
11. plan your own day-to-day activity within the framework of the agreed programme of work, to allow timely completion; and
12. liaise with colleagues to build contacts, exchange information and form relationships for future collaborations.

 

Qualifications 

To apply to this position, it is essential that you:

1. have a Bachelor’s or Master’s degree in the Natural Sciences, Computer Science, or Applied Mathematics; or a Diploma in Computing from a higher education technical school;
2. demonstrate foundational computing knowledge and experience, with fluency in:
       a. the structure and interaction between computer hardware and software;
       b. Linux/Unix command-line;
       c. Bash scripting;
       d. command line data manipulation (grep, awk, sed, etc);
3. have programming experience, with a strong track-record in:
       a. at least one programming language;
       b. Python or R required;
       c. other desirable languages include C#, C++, Java and Javascript;
4. show experience of modern software deployment techniques, including:
       a. working on HPC systems with schedulers (e.g., SLURM);
       b. modern software development, deployment and DevOps;
       c. container systems (e.g., Docker, Singularity);
       d. continuous integration (CI), versioning and deployment of source code;
       e. unit testing of code modules, integration testing with external data sources and achieving this in a CI setting;
       f. bug reporting and contributions to open source repositories;
       g. automation of computational workflows (e.g., Nextflow, SnakeMake);
       h. packaging repositories (e.g., conda, pip, apt, bioconda and dockerhub);
5. demonstrate ability to manage software and data, such as:
       a. a portfolio of work (e.g., thesis project);
       b. well-organised code (e.g., git repos, software packages, ipython notebook);
       c. well-defined use of scratch areas, disk quotas, and long-term archiving;
6. have a proven ability to work with integrity and accountability so that scientific results are easily tracked and reproduced by others;
7. show creativity in solving problems independently;
8. show the ability to work in a team with diverse technical expertise towards a common goal;
9. be committed to equal opportunity and working harmoniously with colleagues of all cultures and backgrounds;
10. have excellent communication skills;
11. be fluent in English.

To be a competitive candidate, it is beneficial if you:

1. know about basic biological principles and research techniques, especially molecular biology, molecular evolution and genomics;
2. are experienced in handling genomics data, such as analysing genome sequence and high-throughput sequencing datasets;
3. have computational biology skills, including comparative genomic analysis, examining gene expression changes and identifying gene regulatory regions.
4. can use a wide range of software and online resources for genomic analysis.

Report to 

You will report to Professor Nicholas Luscombe

Starting Date 

1 September 2021 onwards

Term & Working Hours 

Full-time, fixed-term appointment for 18 months including a 3-month probationary period (inclusive). The contract may be renewed.

Working hours 9:00-17:30, 5 days/week.

Compensation & Benefits 

You will receive a salary set in accordance with the OIST Employee Compensation Regulations.

You will also receive the following benefits:
- Relocation, housing and commuting allowances
- Annual paid leave and summer holidays
- Health insurance (Private School Mutual Aid http://www.shigakukyosai.jp/ )
- Welfare pension insurance (kousei-nenkin)
- Worker's accident compensation insurance (roudousha-saigai-hoshou-hoken)

How To Apply 

Send your application to nicholas.luscombe [at] oist.jp and charles.plessy [at] oist.jp.

(Please replace [at] with @ before using this email address)

 

Submission Documents 

The application should be a single PDF document and include the following:

1. cover letter
2. curriculum vitae
3. names and contact information of 3 referees


* Please indicate where you first saw the job advertisement.
* Prior to the start of employment all new hires are required to successfully complete a background check. Personal information including employment history and academic background should be submitted to third-party administrators after a conditional offer of employment.

Application Due Date 

15 June 2021 (applications will be screened upon arrival). Interview process Online interviews are planned for late June and early July 2021. The process will include a coding test, a panel interview and one-to-one meetings with lab members.

Declaration 

  • OIST Graduate University is an equal opportunity, affirmative action educator and employer and is committed to increasing the diversity of its faculty, students and staff. The University strongly encourages applications from underrepresented groups.
  • Information provided by applicants or references will be kept confidential, documents will not be returned. All applicants will be notified regarding the status of their applications.
  • Please view OIST policy for rules on external professional activities
  • Further details about the University can be viewed on the OIST website www.oist.jp.