Participate in exciting projects with significant impact on the scientific community.
Positions: Scientific Software Developer (UCSD) | DevOps Lead (UCSD) | Postdoctoral Researcher (UCSD) | Biocurator (Rutgers) | Senior Scientific Web Application Developer (Rutgers) | Front-end Scientific Application Developer (Rutgers)
Scientific Software Developer (UCSD)
The RCSB PDB is seeking a Scientific Software Developer with skills as a seasoned, experienced bioinformatics programming professional and a broad understanding of computational algorithms.
The incumbent will develop, implement, and maintain complex scientific and web-based software systems for the RCSB Protein Data Bank (PDB; http://www.rcsb.org) at the University of California San Diego (UCSD).
The Scientific Software Developer will work closely and collaboratively with other software developers and scientists at the San Diego Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand RCSB.org's functionality and reliability as a premier biological data and information resource. S/he will develop new scalable algorithms for the mining and analysis of the rapidly growing PDB archive using leading edge Big Data technologies, design and implement user interfaces for the query, analysis, reporting, and visualization of 3D structural information and associated annotations, as well as integrate external database resources with RCSB PDB to provide a structural view of biology. The incumbent will help lead the design of databases and data warehouses to store and aid in the query of data and be actively involved in the software development process, maintenance and system standards for analysis algorithms, tools, and infrastructure.
Additionally, the incumbent will serve as an expert on relevant scientific and technical aspects of the various web, web services, and database components of the RCSB PDB. S/he will stay abreast of the latest development in structural and computational biology and new technologies, apply advanced bioinformatics concepts to design, develop, modify, debug, and evaluate highly complex software programs and web tools, and translate scientific problems into scalable and maintainable software solutions that meet end-user needs. The incumbent will also further science through Scientific Publications, written in collaboration with our team.
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DevOps Lead (UCSD)
The RCSB PDB is seeking a lead for all IT-related activities as part of UCSD operations. This position will include collaborating with project leads at Rutgers and contributing to the overall strategic planning for RCSB PDB bi-coastal IT solutions.
The successful applicant will be a seasoned, experienced systems infrastructure professional with a full understanding of industry best practices and procedures and will be required to resolve a wide range of issues that are moderately complex in scope. The Dev/Ops lead will evaluate (including simple to moderate cost/benefit analyses) new technologies in order to select solution-focused methods and techniques.
Additionally, the incumbent will take lead responsibility for cloud instance (OpenStack and Docker/Kubernetes) system administration; maintain and further develop automation and orchestration tooling for all RCSB services; perform cost-benefit analysis of new service and solution infrastructure designs, prototype their deployment, benchmark the results, and manage their deployment into production. It is expected that these tasks will be perfomed with minimal supervision.The Dev/Ops lead will proactively provide uninterrupted service for all PDB production services 24/7/365, identify problems and bottlenecks in current systems and specify, design, and execute solutions and lead the transition to containerization of the infrastructure and transition to third party cloud providers.
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Postdoctoral Researcher (UCSD)
We are seeking a talented, highly motivated postdoctoral researcher to join the multidisciplinary team of the RCSB Protein Data Bank at UC San Diego, San Diego Supercomputer Center (SDSC).
The successful applicant will work on research projects that drive next generation search tools at rcsb.org. Dealing with redundancy within the Protein Data Bank (PDB) is an important challenge in face of the ~10% year-on-year growth in structural data stored in the PDB. Tackling the redundancy problem requires understanding of similarities and differences among macromolecules at many different levels. She/he will be expected to contribute to this project by devising new and improved algorithms for protein family classification at levels such as biological assemblies. The ultimate aim of this project is to improve the findability of data in the PDB by building the next generation search engine for structural molecular biology.
Note, this position is reviewed annually on the basis of performance and can be renewed.
Qualifications: Ph.D. in one of the following research areas
- Computer Science with a focus on Bioinformatics
- Structural Bioinformatics, or related field with a focus on software development
- Structural Biology with a focus on software development
- Demonstrated proficiency in a high-level programming language, such as Java, Python, C++, and experience with state of the art software engineering tools.
- Strong skills in problem solving and algorithm design are required.
- A background in NoSQL database technologies would be beneficial.
- Experience in development of modern web applications, user interface design, or scientific visualization would also be a plus.
- We expect candidates to have shown high productivity demonstrated by publications and contributions to open source software projects.
- Excellent written and oral communication skills are required.
For more information, click here.
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Biological Structure Annotation Specialist - Biocurator (Rutgers)
Deposition/Biocuration Services provide expert deposition, validation, biocuration, and remediation services to Data Depositors worldwide, maintain data quality and uniformity in the PDB archive which is critical to research and education, develop and promote community-endorsed data standards for archiving and exchange of global structural biology data.
- Analyze, curate, and validate macromolecular structures from the PDB community
- Participate in exciting projects with significant impact on the scientific community
- Communicate daily with members of the research community
- Participate in fun outreach activities
Why join us:
- We ensure PDB data are Findabile, Accessible, Interoperabile, and Reusable (FAIR) by providing expert data curation which is critical for biological data resources.
- We provide friendly working environment and excellent professional development opportunities.
- At Rutgers, this academic position offers New Jersey state benefits and a faculty-level salary.
Knowledge and skills:
- Experience in structural biology with a PhD in a relevant field required
- Strong knowledge of small molecule chemistry or cryo-electron microscopy (3DEM) preferred
- Experience in bioinformatics, cheminformatics, or computer scripting would be an advantage
The successful candidate should be self-motivated, pay close attention to details, possess strong interpersonal communication and writing skills, and have the ability to handle multiple projects.
For more information, see:
- wwPDB biocuration supporting open access to high-quality 3D structural biology data (2018) Database 2018: bay002 doi: 10.1093/database/bay002
- The rewards of working as a data wrangler Science Careers doi: 10.1126/science.caredit.aaq0481
Senior Scientific Web Application Developer (Rutgers)
We are looking for a full-stack developer with a minimum of five years experience using modern database and web technologies. The candidate should enjoy engaging with other developers and scientists in a collaborative team environment.
The work at the PDB focuses on data analysis and transformation, and the presentation and visualization of data using complex interactive graphical user interfaces. An important aspect of the work is to provide our users with the ability to search and explore the data in the PDB Archive. Solutions are implemented using a wide range of custom components developed and maintained at the RCSB PDB, in addition to third-party tools, libraries, frameworks and technologies.
The candidate should be comfortable working in a fast-changing environment, and be able to demonstrate an ability to think creatively, generate new ideas, and implement solutions. The candidate should also show an eagerness and willingness to learn new skills and master new technologies.
The team at RCSB consists of a group of highly-skilled bio-curators, scientists, software developers, designers, and educators, working in a lively and fast-paced environment.
The successful candidate will be able to take full advantage of the benefits of working at an academic institution. Employees are encouraged to engage in professional development, either by attending seminars and training workshops, or by enrolling, tuition-free, in courses provided by Rutgers.
Ideally the candidate should have in-depth experience with several of the following technologies, languages, and frameworks, or have experience with comparable or related technologies:
Any scientific background would be considered a plus, especially experience in any of the following areas: Molecular Biology, Bioinformatics, Biochemistry, Chemistry, Genomics. Experience working with large and complex scientific datasets would also be a plus.
While a scientific background is not a requirement for the position, the candidate should be able to demonstrate a willingness and ability to engage with scientists and scientific content, and be interested in working in an academic/research environment.
Responsibilities for this position will include:
- Design, development and deployment of modern, scalable, reusable web-applications.
- Analysis, refactoring and adaptation of legacy code to conform to new architecture designs.
- Development of complex interactive graphical user interfaces.
- Debugging, testing, troubleshooting.
- Use of and development of automated testing suites.
- Masters or B.Sc degree in Computer Science, Biochemistry, Bioinformatics, or a related discipline, or a comparable combination of education and experience developing modern Scientific Web applications.
- Excellent interpersonal, verbal and written communication skills.
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Front-end Scientific Web Application Developer (Rutgers)
The ideal candidate should consider themselves to be expert in the use of current web technologies. The candidate should be able to engage with other developers in a collaborative team environment, generate ideas, design and build solutions and show a willingness to master new skills and technologies.
The successful candidate will focus on:
- Design, development and deployment of modern, scalable, reusable, and cross-platform front-end software
- Development of complex interactive graphical user interfaces
- Refactoring and adaptation of legacy code to conform to current architecture requirements.
- Debugging, testing, and troubleshooting of web applications using browser-based tools and automated testing suites
This individual must work onsite at RCSB PDB located at Rutgers, The State University of New Jersey.
Minimum Education and Experience
- While a scientific background is not a requirement for this position, any background education or experience in chemistry, biology, structural biology, bioinformatics, or related fields would be considered a plus.
- Any experience working with large and complex data sets would also be considered a plus.
Required Knowledge, Skills, and Abilities
- Experience working with relational and/or document databases (e.g. MySQL, MongoDB)
- Experience using any of the following languages, technologies, and frameworks:
- HTML, CSS, JSON
- React/Redux, NodeJS, JQuery
- Use of Git and modern IDEs.
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About RCSB PDB
RCSB PDB is a world-renowned, scientific organization focused on serving technical, educational and other programmatic needs of scientific and research communities worldwide. RCSB.org serves more than 1 million users in academia and industry. The RCSB PDB development team, located at UCSD/SDSC and Rutgers, creates leading edge web technologies targeted for scientific and educational audiences.
About Rutgers, The State University of New Jersey
RCSB PDB is located at the Institute for Quantitative Biomedicine at Rutgers in Piscataway, NJ.
Rutgers, The State University of New Jersey, is a leading national research university and the state of New Jersey’s preeminent, comprehensive public institution of higher education. Established in 1766, the university is the eighth oldest higher education institution in the United States. More than 70,000 students and 23,400 full- and part-time faculty and staff learn, work, and serve the public at Rutgers locations across New Jersey and around the world.