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Created 2015-04-08 01:10:19 | Updated | Tags: job job-offer support
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You've got basic experience with GATK, MuTect, Picard or related genome analysis tools, and a burning desire to help enable great science for a living? Join us now by applying for job #1774 on the Broad careers web page.

The job in a nutshell:

  • Work closely with method developers and software engineers to ensure user proficiency with analysis software, diagnose and/or resolve user issues, and provide scientific/technical support;
  • Create and maintain web-based technical documentation, tutorials and FAQs;
  • Organize workshops to train users in best practices and general workflows;
  • Perform analyses demonstrating the value of the tools for the user community.

But don't be fooled by the dry description -- this job offers variety, challenge and plenty of opportunity for growth. See my personal perspective/pitch below!


If you're a regular here, you may know I joke about being a glorified tech support monkey sometimes, but let me assure you that this job -- this team -- is about much more than that.

We are currently a team of three -- Sheila (associate computational biologist), David (senior technical writer) and me, Geraldine (bioinformatics scientist, formerly wetlab microbiologist).

As the support and outreach crew for GATK, it's up to us to make sure that the user community -- tens of thousands of researchers worldwide -- has the tools and understanding they need to go out and perform great research. Quite a bit of that research has direct impact on patient outcomes, real human lives (see the user stories for some examples). Some of it follows a more fundamental-knowledge path, and that's great too; it all goes to building up the edifice of scientific knowledge. I sincerely believe that we actively contribute to that research by equipping the community with the right information in the right format.

That is heck of a challenging task. It involves fielding questions from individuals from all sorts of backgrounds (from pure biology to pure computer science) with all sorts of questions (from experimental design to details of algorithms, with a splash of hardware optimization on the side) coming from all sorts of language backgrounds that can complicate communication (I'm originally francophone, myself). And that's just one side of the equation. On the other side, we're working closely with the development team, who are also very heterogeneous: we have software engineers, mathematicians, at least one former hedge fund quant, computational biologists, statisticians, and plenty more besides. All with their own particular perspectives that inform how they communicate about their work, which we then need to boil down into actionable information tailored for the researchers who use the software. So we do a lot of translating of all kinds!

And it's not just back and forth questions and answers or writing documentation, either. Personally, some of the parts that I like best about the job are the opportunities to directly influence the software design and feature set, which typically lead to improved usability and applicability of the tools, based on feedback from users and in-depth discussions with the developers. I always wanted to get into software development and never had any properly relevant qualifications, so it's a real treat to feel involved in that part of the process. Sometimes I even get to contribute minor features or bug fixes myself, which is way cool.

Finally, I can't not mention workshops -- especially the invited workshops held in exotic foreign lands, like, um, Belgium (hey don't knock it, that's where I'm from). Also, Thailand, the UK, and soon, South Africa! These workshops typically involve a team of three people (typically one from the support team and two developers) traveling to the host institution and teaching a multi-day workshop. Some of those who participate originally do it for the free travel; all end up really enjoying the immensely rewarding experience of meeting our users in person. GATK users are on average an absolutely lovely bunch of people, and it's really fun to get to spend a few days interacting, teaching and collecting feedback.

Okay, there's still plenty more to it but I've already gone on too long, so if you want to know more, just apply or message me!


How to apply: got to the Broad careers web page, just enter 1774 in the "requisition number" box and don't worry about the rest.


Created 2014-11-24 20:55:06 | Updated | Tags: jobs job-offer cancer
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We're advertising this job on behalf of our colleagues in the cancer analysis team. See the overview below the fold. If you're interested, please message me (@Geraldine_VdAuwera) or apply on the Broad's careers page (search for job requisition number 1591).

Please note that this job requires on-site presence (no remote work) and Broad cannot offer visa sponsorship for this opportunity.


Overview

Part-time opportunity to make a contribution to The Cancer Genome Atlas, a project with global impact in the search for a cure for cancer. Work with world-class researchers at the Broad Institute to publish large datasets generated by computational algorithms. Assist with development and maintenance of automated pipelines.

Part-time twice a week, on-site at the Broad Institute.

Characteristic Duties:

  • Assist cancer genome analysts in preparing data submissions to make available to the TCGA research community.
  • Generate automated data submissions for the TCGA research community.
  • Identify and address technical issues with automated pipelines.
  • Extend the functionality of automated pipelines.
  • Assist with documentation of automated pipelines.
  • Work with project managers to ensure that requirements and timelines are being met.
  • Work with engineers on process or design issues

Requirements:

  • Bachelor Degree or currently enrolled in a Bachelor Degree program. Computer Science, Computational Biology, or Bioinformatics preferred
  • Proficiency in linux or other unix flavor
  • Python experience a big plus
  • Knowledge of web services a plus
  • Prior involvement or interest in genomics a plus
  • Excellent communication skills

Created 2014-08-28 21:23:53 | Updated | Tags: developer job-offer topstory
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We're looking for a developer (software engineer or equivalent) to join our team on a part-time basis as a software engineering consultant.

The mission is to take on tasks that are non-critical but still important, such as fixing bugs and implementing minor feature requests, usability improvements and so on in the GATK codebase. The idea is to take much of the maintenance burden off of the core development team so they can focus on developing new tools and methods.

We already have one person employed in this capacity, and it's working out very well. However there is quite a bit more to do than he can find time for, and therefore we'd like to hire a second consultant to pick up the extra work in parallel. (We were hoping to just clone him but ran into some difficulties getting IRB approval.)

This position does not require expert knowledge of GATK, but familiarity with the GATK tools is a big plus. The main language is Java, with a small side of R and Scala. We also have a growing corpus of C++ code that is not yet in the scope of this position, but may move into scope some months down the line.

Note that this opportunity is amenable to remote work so you don't need to be local to the Boston area, but it is limited to US residents with valid work authorization (no H1B sponsorship possible, sorry).

Drop us a line in the comments below or private-message me (@Geraldine_VdAuwera) to discuss details.


Created 2014-04-14 21:00:52 | Updated 2014-04-14 21:01:34 | Tags: paper job job-offer
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We have a problem: we have a truckload of material sitting around waiting to be published, but no time to actually write the papers. So we're looking for someone who will help us convert this computational biology goldmine into cold hard Nature Biotech/Methods papers.

This is a great opportunity for an early-career, postdoc-level scientist who has experience publishing papers, demonstrated writing ability, and is not afraid of wrangling complex technical material.

Make no mistake, we're not looking for a ghostwriter; this will involve intellectual contribution worth the authorship in high-profile publications. But the basic material is ready and waiting.

Here is the complete job description; feel free to ask questions in the comments or by private message to me (Geraldine):


Scientific Technical Writer

The Genome Sequencing and Analysis group seeks a scientist with excellent writing skills and experience with scientific publication to work with scientists and engineers on transforming notes and technical documentation for existing analytical methods and tools into polished papers aimed at high-profile journals such as Nature Biotechnology and Nature Genetics. In collaboration with researchers working at the forefront of bioinformatics, including the group that develops the gold-standard Genome Analysis Toolkit (GATK), the writer would be responsible for designing paper structure and identifying necessary content to (1) better explain the theory that underlies methods and tools and (2) powerfully illustrate use cases based on public datasets. The writer would focus their writing on the introduction, results, and discussion sections of the papers, expanding existing technical material, while the team will provide the methods sections.

The writer will be hired as a consultant, with a minimum of 20 hours/week of work (more hours are possible if desired).

Requirements:

  • Ph.D. in a scientific discipline (not necessarily bioinformatics or computational biology, though familiarity with those fields is helpful);
  • experience and skill in writing scientific papers (experience with other scientific writing activities, e.g., grant-writing, is also helpful);
  • ability to craft a logically structured text from unstructured material;
  • ability to synthesize information from diverse sources;
  • ability to write clearly and concisely without sacrificing precision;
  • ability to communicate effectively in a team setting;
  • ability to work in a highly collaborative team environment; and
  • desire to take direction and iterate drafts with team members.

Created 2013-09-25 22:35:26 | Updated 2013-09-27 14:14:43 | Tags: official jobs job-offer compbio
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Yep, we're hiring again; we need even more compbios!

Do you dream of working on challenging problems, in a stimulating environment with plentiful resources? Or do you simply love the GATK and wish you could spend every waking moment playing with it? Good news! We have a position open for a computational biologist to join our team. You can find out more about us on this page. The job itself? In a nutshell, help develop and apply methods in NGS to medical genetics projects. You can find more details in the Broad Career Center -- look for Requisition Number #1107.

If you're interested (and who wouldn't be?) please message @rpoplin directly. That's Ryan Poplin, now leader of the Computational Methods Development group since Eric Banks became big chief of GSA last week.

We are of course happy to answer questions here in this thread about what it's like to work in the GSA group (awesome!) and how interesting it is to work on the bleeding edge of genome research (amazing!). Feel free to private-message us about it if you don't want your supervisor to know that you're thinking of jumping ship ;-)


Created 2013-07-25 19:33:27 | Updated | Tags: official job-offer compbio
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Do you dream of working on challenging problems, in a stimulating environment with plentiful resources? Or do you simply love the GATK and wish you could spend every waking moment playing with it?

Good news! We have a position open for a computational biologist to join our team. You can find out more about us on this page, and a detailed job description on the Broad's recruiting webpage here (search for job requisition #1107).

If you're interested (and who wouldn't be?) please apply directly on the jobs webpage. The Broad's lovely HR people will handle your application and answer any questions you may have about the hiring process and employment conditions.

We are of course happy to answer questions here in this thread about what it's like to work in the GSA group (awesome!) and how interesting it is to work on the bleeding edge of genome research (amazing!). Feel free to private-message us about it if you don't want your supervisor to know that you're thinking of jumping ship ;-)


Created 2012-08-20 18:31:36 | Updated 2013-01-07 20:46:20 | Tags: job-offer
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Hello, My name is Olguine at TAJ Technologies Inc (www.tajtech.com), Headquartered in Minnesota. TAJ is an IT consulting firm that specializes in providing premium technology solutions across a variety of industries. For over two decades, we’ve been providing technology staffing, consulting and project-based services to a number of distinguished clients.

One of these clients is a world renowned, non-profit medical practice and research group that has several locations throughout the U.S. This clinic is recognized as a leader in treating advanced diseases, ones often mistreated because of their complexity. Its “patient-first” mission has earned them top rankings in the U.S. News and World Report’s Best Hospitals for the past 20 years.

Listed below is a description of the position, followed by job qualifications and required skills. If you are still interested in the opportunity, please let me know when would be a suitable time to contact you for a brief chat. I look forward to speaking with you. Title: Bioinformatics Specialist Location: Rochester, Minnesota Duration: 24 Months with possibility of Long Term

Description: Seeking to hire an Individual with Bioinformatics-Sequencing experience. The Employee will develop software and infrastructure for supporting nextgen sequencing analysis under the supervision of an Informatics Lead or designated senior level Informatics Specialists. Other responsibilities are to provide application development and testing support for bioinformatics unit, including testing and development of genomics-related projects develops scripts or software applications to support data management, data extraction, data integration and data analysis as required. An ideal Candidate should be knowledgeable in the handling and in the design of repository systems to contribute to the development of internal databases. The Candidate will have basic expertise in the informatics methods used to analyze data, interpretation of data analysis, writing reports, and contribute to the design of analytical procedures and execute analytical procedures in the framework of a specific project. A qualified candidate should have a degree in domain informatics (computational biology, computational chemistry, bioinformatics, clinical informatics, medical imaging, and medical informatics), and domain-relevant science experience in biology, chemistry, mathematics, physics, statistics, or health sciences. Proficiency building software applications using high level programming languages (java/c + +) and working in Linux environment is required.

Education: Master’s in Bioinformatics (Computational Biology, Chemistry, Clinical Informatics, Medical Imaging, Mathematics, Physics, Statistics, Or Health Sciences) Location: Rochester, Minnesota Duration: 2 years to Long Term Position

Required Skills Genomic or Genetic Domain Experience 3 years Galaxy Experience with front end data analysis tools Experience using CLCBIO, GATK, and BioSQL Tools Java development experience (average or above) 5 years Familiarity with XML and xml parser (java) 5 years Database Experience 5 years Websphere Experience 5 years RAD Experience 2 years Web Service 2 years Analyst Skills 2 years R/SAS Statistics 2 years Working experience using XSL (EXtensible Stylesheet Language) and XSLT (XSL transoformation) Experience with testing using junit test framework Working experience with Linux and windows Experience with Linux shell script Experience with web development would be useful

Email: olguine.o@tajtech.com "TAJ Technologies Inc is an EEO/AA Employer"


Created 2012-08-08 16:22:35 | Updated 2013-01-07 20:47:52 | Tags: personalis job-offer
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Hello all,

My sister company Bereina has been retained by Personalis, a young startup in Palo Alto, CA, to help recruit for their open positions. Personalis’ goal is to use genome sequencing technology to develop products for clinical research and medical diagnostics. Their team is still fairly small right now, but they are looking at consistent growth for the foreseeable future.

Currently they are seeking bioinformatics engineers and scientists for their platform and applications teams, and one of the key traits they are prioritizing is experience with GATK. As this is a forum for GATK discussion, I thought it might be a good place to post about this. Some of the other skills they are looking for include experience with Python, Java, C++, and R.

I’ll try to keep this updated with information about the current openings. If anyone has any questions, feel free to ask, and I’ll do my best to ask answer thtem. I can also pass along resumes for review, so if you are interested, please send them to thomas@nwsecurecheck.com.