News

New Opportunities at the PDB

The RCSB Protein Data Bank at Rutgers University is looking to fill three new positions described below.

  1. 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.

Apply at UCSD: https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=104863

 

  1. 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.

Requirements

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

Qualifications

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.

Apply at UCSD: https://apol-recruit.ucsd.edu/JPF02453

 

  1. Scientific Web Application Developer (Rutgers)

Research Associate

Summary

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.

Requirements

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:

Relational and document databases (MySQL, MongoDB), search tools (ElasticSearch, GraphQL), Java, Python, Javascript, JSON, React/Redux, Node.js, JQuery, HTML, Git, shell scripting, use of modern IDEs.

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.

Job Description

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.

Qualifications:

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.

Apply at Rutgers: jobs.rutgers.edu/postings/105869

ASU professor awarded top research prize

The Royal Swedish Academy of Sciences has awarded the prestigious Gregori Aminoff Crystallography Prize, one of the physics research community’s highest honors, to Arizona State University Regents Professor John Spence.

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Lattman, Liu, Morrow and Ruhl elected AAAS fellows

Four University at Buffalo professors have been elected fellows of the American Association for the Advancement of Science (AAAS), the world's largest general scientific society and publisher of the journal Science.

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Job Openings - UB & HWI

The Hauptman-Woodward Medical Research Institute attracts talented scientists and support staff to explore exciting research opportunities and the freedom to pursue the unknown. We offer an excellent benefits package including health insurance, generous retirement plan, disability, and life insurance coverage, competitive vacation/holiday policies, and pre-tax spending accounts. The Institute is a welcoming environment and embraces diversity in people as well as the skills they bring to us.

Current Openings:

Postdoctoral Associate

A Postdoctoral Associate position is available based at the Hauptman-Woodward Medical Research Institute (HWI) and affiliated with the University at Buffalo. We are looking for a highly motivated structural biologist with an interest in metalloproteins and methods development to join a project with the Snell and Bowman laboratories involving the structural study of biological systems that are impacted by free radical activity and metalloproteins, where the modeled metal and/or coordination state are of interest for further investigation. The work will involve a collaboration with laboratories at Stanford and Oxford and will use X-ray crystallography, UV-spectroscopy, and micro-PIXE techniques. The eventual aim involves structural studies using X-ray free-electron sources for radiation chemistry-free data. It is possible that neutron studies would also take place. The position involves working directly with the Crystallization Center at the Institute and will have access to a Glacios cryo-EM with Falcon 4 detector. The Institute runs the IMCA beamline at the Advanced Photon Source. It is anticipated that multiple structural techniques will be employed, and while the candidate should have structural biology expertise, they are not expected to be proficient in all structural biology techniques. Molecular biology expertise is required to produce target proteins and complexes. Many techniques will be employed.

This position is based at HWI but offered through the University at Buffalo. Application instructions and details are available at the University of Buffalo job posting site.

Research Scientist

BioXFEL is an NSF Supported Science and Technology Center developing the biological applications of X-ray Free Electron Lasers. It is a consortium of 8 institutions led by staff from the Department of Materials Design and Innovation (MDI) at the University at Buffalo, State University of New York (UB), and administratively headquartered at the Hauptman-Woodward Medical Research Institute. One of the teams in BioXFEL provides data processing support for XFEL experiments around the world. We are looking for a research scientist that can join this team and provide data processing support for crystallographic and potentially solution and single-particle XFEL experiments. The support functions would be based in Buffalo with the opportunity to attend some beamtimes if necessary. The support team consists of staff from multiple BioXFEL institutes. We are looking for a candidate who can operate effectively in a diverse community of students and investigators who shares our vision of helping all constituents reach their full potential.

The successful candidate(s) will be involved with the following:
• Assisting in data processing for crystallographic based XFEL experiments.
• Assisting in the analysis and drafting of publications related to results.
• Establishing expertise to help support potential single-particle and solution-based experiments.
• Helping teach others best practices for data processing.
• Contributing to the scientific development of new techniques and methodologies dependent on level and experience.

The candidate would be based at the Hauptman-Woodward Medical Research Institute in Buffalo New York but work closely with UB, HWI, and BioXFEL scientists and students as part of the effort. This position is based at HWI but offered through the University at Buffalo. Application instructions and details are available at the University of Buffalo job posting site.

 
EEO Statement

The Hauptman-Woodward Medical Research Institute, Inc. (HWI) as an equal opportunity employer, extends employment opportunities to qualified applicants and employees on a non-discriminatory basis without regard to race, color, sex, creed, age, religion, national origin, marital status, veteran status, sexual orientation, genetic predisposition, carrier status, or disability that would prevent the performance of the essential requirements of the job with or without a reasonable accommodation in compliance with the appropriate New York State and Federal laws, or any other legally protected characteristics. This policy applies to all conditions and terms of employment.

European XFEL Virtual User Information Meeting - 7th Call for Proposals

European XFEL Virtual User Information Meeting  - 7th Call for Proposals

 

virtual information meeting will be hosted by the European XFEL User Organization Executive Committee (UOEC) and held on

 

25 November 2020 17:30-19:30

(Hamburg/Schenefeld local time - CET)

 

The event will specifically address our 7th Call for Proposals - open until 16 December 2020 (16:00 CET).

Speakers will take immediate questions after every talk and a Q&A session is planned at the end of the event.

 

All prospective proposers are encouraged to attend!

Please click the link below to join the virtual event:
https://xfel.zoom.us/j/91097953348?pwd=YWpLcHRKcXFIeDBNSGR3ME9xU0xJZz09
Passcode: 351364

Meeting ID: 910 9795 3348

International telephone numbers available:

https://xfel.zoom.us/u/ad8w4NVPGV

 

UOEC Moderators:

Marion Harmand (IMPMC, France) and

Robert Grisenti (GSI Helmholtzzentrum für Schwerionenforschung, Germany)


Agenda


1. Welcome
2. Facility update (10 + 2 mins) (S. Pascarelli)
3. Call for proposals (10 + 2 mins) (S. Pascarelli)
4. Short updates on run 202102 from each instrument (10 mins + 2 mins each)
-        FXE (C. Milne)
-        SPB/SFX (A. Mancuso)
-        HED (U. Zastrau)
-        MID (A. Madsen)
-        SCS (A. Scherz)
-        SQS (M. Meyer)
5. Open for questions (20 minutes)

 

Other panelists, available for questions:

S. Aplin (Science Support Data Department), S. Bertini (User Office), R. Feidenhans’l (Managing Director), S. Molodtsov (Scientific Director), H. Sinn (Science Support Instrumentation Department)

New Positions at UC Merced

UC-Merced

The Thompson Lab at University of California Merced is recruiting a Postdoctoral Scholar and a Junior Research Specialist:

The Postdoc will work on projects related to multi-temperature and time-resolved (T-jump) crystallography at synchrotrons and XFELs. Job posting with additional details here: https://aprecruit.ucmerced.edu/JPF01028
 
The Junior Specialist will support wet lab operations, and assist with a variety of research projects in structural biology (including but not limited to XFEL experiments). Job posting here: https://aprecruit.ucmerced.edu/JPF01024