Job Postings

CMI Research Applications Programmer

Job Description

Under the direction of the CMI Director in conjunction with sponsoring PIs, the incumbent will serve as a principal programmer for the Center, applying skills as a seasoned, experienced software professional with a full understanding of industry practices, community standards and relevant policies and procedures to medium-sized projects or portions of large projects with moderate scope and complexity. Resolves a wide range of issues. Demonstrates competency in selecting tools, methods and techniques to obtain results.

Interacting with CMI researchers, the incumbent will plan, organize and direct the gathering of requirements and subsequent design, development and support of multiple CMI web applications. Design, develop and present prototypes that meet the requirements; turn these prototypes into production quality code; and perform extensive end-to-end testing to verify that system meets performance and reliability. Monitor and support deployed applications during field studies, detecting and correcting operational problems and resolving problems as required.

CMI labs develop a broad range of web-based and mobile applications that are critical to its research mission. For example:

• LabMan, a web-based platform to help and accelerate sample processing in the web lab by generating the processing sample plates and keeping track of all components and machines available in the laboratory. LabMan’s requirements were initially defined by the wet lab members of the Knight Lab and will be expanded by other members of the CMI.

• Qiita is an open-source web-based platform that enables non-bioinformaticians to perform their own metagenomic analyses and meta-analyses easily using standardized pipelines such as such as Qiime2 and GNPS. Qiita’s requirements and improvements are guided on the expectation of its users and delivered by monthly releases. Qiita’s users ranges from experienced bioinformaticians doing complex meta-analysis to biologist, ecologist or clinicians processing their first study.

• Metadata Wizard, an open-source web-based platform to enable researchers to create rules and descriptions of their metadata to create Qiita-compliant sample information to streamline downstream analyses and metaanalyses for microbiome-related research projects. 

• Global Natural Products Social Molecular Networking (GNPS, https://gnps.ucsd.edu/), a web-platform provides public data set deposition and/or retrieval through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository. The GNPS analysis infrastructure further enables online dereplication, automated molecular networking analysis, and crowdsourced MS/MS spectrum curation. Each data set added to the GNPS repository is automatically reanalyzed in the next monthly cycle of continuous identification.

The web applications programmer will also have the opportunity to work with graduate students, postdoctoral fellows and staff scientists to create new tools to advance microbiome research and to promote a deeper integration of tools to address multi-omic analyses.

Apply by April 27, 2018 for consideration.

Qualifications

  • A Bachelor's Degree in related; area and/or equivalent experience/training.

  • Proven experience with programming in a linux environment using SQL databases as well as experience programming web pages for web-based applications using Apache/Tomcat.

  • Demonstrated experience in Java and Python. 

  • Demonstrated experience with relational databases: PostgreSQL and MySQL. 

  • Experience with variety of software applications such as Microsoft Office, Project ,Visio, Visua Studio and Eclipse.

  • Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts. 

  • Demonstrated experience designing web-based user interfaces. 

  • Ability to understand functional needs and how systems can support those needs. Ability to develop conversion and system implementation plans.

  • Demonstrated broad problem solving skills.

  • Intermediate knowledge of secure software development.

  • Demonstrated ability to interface with management on a regular basis.

  • Proven ability to contribute technical narrative to grant proposals.

  • Solid experience with identification and use of code libraries and open-source forums.

  • Experience with planning for deployment and creation of feedback mechanisms.

  • Demonstrated software repository skills. Testing and test planning skills.

  • Strong experience with common programming tools. Ability to follow software specifications.

  • Ability to communicate technical information to technical and non-technical personnel at various levels in the organization.

  • Demonstrated effective communication and interpersonal skills.

  • Self-motivated and works independently and as part of a team. Able to learn effectively and meet deadlines.

Positions available in the Chu Lab at UC San Diego

Hiu Chu is new to UC San Diego and CMI, previously with Sarkis Mazmanian at Caltech. Her focus is on the microbiome using gnotobiotic mice in her new lab at ACTRI - and she's hiring! See below for an excerpt from her lab website:

 

  • Lab Manager & Research Technicians: We are currently accepting applications for a Lab Manager or Staff Research Associate. This position will have the opportunity to lead and participate in research projects while managing a dynamic new lab. If interested, please email Hiu with your CV and three references, and a brief summary of your leadership & management style. Excellent organizational and communication skills are required.

 

  • Postdocs: We are actively recruiting post-doctoral fellows who have a strong interest and/or prior training in immunology or microbiology. To apply for a postdoctoral fellowship in the laboratory, please send your CV with a statement of interests and three references to Hiu.

 

  • Graduate students: If you are a UCSD graduate student looking for a lab, email Hiu and we can set up a time to meet. We are always seeking inspired, enthusiastic, and curious graduate students to join our group! For prospective graduate students interested in the lab, please see the Biomedical Sciences website to apply for the graduate program.

 

  • Undergraduate students: Outstanding and inquisitive undergraduate students are welcome in the lab. Ideally, students interested in research should join the lab no later than their sophomore year, but all candidates will be considered. Please contact Hiu with your prior experience, relevant coursework, and an estimate of how much time you plan to spend in lab (hours/week).

 

Intheon - Scientists and Engineers

Company Overview

Intheon (formerly Qusp Neurotechnologies), is seeking highly talented and motivated research scientists and engineers to work with our team in San Diego on technology that will power the coming generation of brain-based human-machine interfaces, integrating neurotechnology into everyday life. We are building the first comprehensive, cloud-scalable, middleware platform for real-time processing of neural and other biosignals, using advanced machine and deep learning algorithms, multisensor data fusion strategies, and online signal processing techniques to provide real world neuronal and cognitive state assessment. We are also actively engaged in cutting-edge fundamental and applied clinical, computational, and cognitive neuroscience research and development through collaborations with leading academic institutions and federal research agencies.

We are presently looking to fill three positions, briefly summarized below.

For further details on each position, specific requirements and application instructions, please visit the jobs page on our website (www.intheon.io/jobs), or on Indeed.com.

We look forward to hearing from and working with you!

** Deep Learning Research Engineer

You are experienced in designing and implementing deep learning algorithms and are looking for the most exciting, challenging, and high-impact areas to apply the latest developments in ML and AI. You will work with our senior research engineers to design and implement advanced brain-computer interface technology using state of the art deep learning techniques. Specifically, you will:

  • develop new methods for applying deep learning on EEG and other physiological data
  • write production-grade code and train Brain-Computer Interface models on large amounts of EEG data

** Neuroscientist (Staff Scientist)

You want to use your expertise and experience in computational neuroscience to develop and apply new cutting-edge technologies for large-scale EEG data analysis, essential for training robust powerful machine learning systems capable of decoding brain state in complex environments. You may also work on projects related to the development and application of novel closed-loop brain-computer interface technologies. Specifically, you will work with our senior researchers to:

  • develop methods to advance the state of the art in large-scale EEG data processing and management
  • develop new computational methods for combining EEG features across multiple studies (meta-analysis)
  • interpret analysis results and publish them in scientific journals
  • develop and apply methods for real-time cortical connectivity analysis and closed-loop neuromodulation

** Senior Software Engineer

You are a versatile software engineer with demonstrated expertise in writing and deploying production software on AWS or similar platforms, as well as writing high-quality desktop code in Python and C/C++. You are excited about applying your experience and skills to cloud- and desktop-based platforms for real-time neural and biosignal processing using advanced deep learning and other algorithms. Specifically, you will:

  • develop and extend new desktop software for advanced biosignal processing
  • develop, extend and deploy biosignal processing software on a robust cloud platform
  • write high-quality production-grade, secure, scalable, and clearly documented code

BASF - Sr. Bioinformatics Team Lead

Job Description

We are seeking a Senior Bioinformatics Team Lead to join BASF’s Computational Chemistry & Bioinformatics group within the global Digitalization in Research and Development function at our site in Research Triangle Park, North Carolina.

As part of an enthusiastic global team of experts, you will support BASF’s worldwide Bioscience Research activities. Your role covers management, coaching and development of the Research Triangle Park (RTP) Bioinformatics team, while providing hands-on scientific project support by directly analyzing genome, metagenome, proteome, transcriptome and various other datasets for in-depth mining and interpretation.

As a team lead you will be responsible for a team of experts in BASF’s worldwide Digitalization in R&D Department providing support to our project partners in all bioscience activities. You will leverage your experience leading teams to advise, coach, and develop a team of bioinformaticians. You will be responsible to develop, apply and evaluate new computational solutions to manage workflow automation, data curation, and data visualization. Your ability to communicate clearly and openly along with your skill at building relationships with our internal project partners is key for project success and continuous advancement of current and future needs. Your solid proficiency in managing projects with diverse groups of participants will be necessary as part of local, regional and global effort in a global bioinformatics team and with cross-functional teams.

This is a challenging assignment with a motivated team in a high-paced, entrepreneurial work environment coupled with excellent opportunities for career development in a leading multinational corporation.

Qualifications

REQUIRED:

  • PhD in Bioinformatics, Computational Biology, Molecular Biology or a related field with >5 years relevant work experience, MS with >8 years of experience or BS with >10 years of experience
  • Proficient scripting abilities and exposure to multiple programming languages
  • 2 years in a leadership role with direct reports
  • Excellent organizational, communication and project management skills
  • Exhibit entrepreneurial drive and a positive team spirit.
  • Must be goal oriented, customer focused and able to work in a fast-paced international team setting

PREFERRED:

  • PhD in Bioinformatics, Computational Biology, Molecular Biology or a related field with at least 5 years Bioinformatics experience
  • Experience leading a team of direct reports in an industry setting
  • Experience working in an industry environment for 5 to 10 years
  • Experience with model plant, crop, and microbial bioinformatics

Scoping Questions

    Required:
  1. Do you have a PhD in Bioinformatics, Computational Biology, Molecular Biology or a related field with >5 years relevant work experience, MS with >8 years of experience or BS with >10 years of experience?
  2. Do you have at least 2 years in a leadership role with direct reports?
  3. Are you proficient in UNIX/Linux and have strong computing skills with Perl or Python?

Preferred:

  1. Do you have a PhD in Bioinformatics or a related field with >5 years of industry experience?
  2. Do you have experience with model plant, crop, or microbial bioinformatics?

BASF - Sr. Team Lead Systems Biology

Job Description

We are seeking an innovative computational scientist to lead BASF’s Systems Biology group at our site in Research Triangle Park (RTP), North Carolina. Your role covers management, coaching and development of the RTP Systems Biology team, while providing hands-on scientific project support. Your leadership skills and past experiences leading teams will be leveraged to organize tasks and communications within your team.

As part of a diverse and innovative global team of experts, you will apply statistical and computational skills to analyze molecular and phenotype data in support BASF’s worldwide Bioscience Research activities. You will draw from novel genotypic, phenotypic, and expression profiling including transcript, protein, and metabolite data to identify product candidates. Your knowledge of novel developments and methodologies in the fields of Deep Learning and Machine Learning will prepare you to develop innovative solutions for the analysis and modeling of complex molecular biological data.

You will play a key role in developing strategy, and in communicating with multiple stakeholders within BASF. You will work closely with other systems biologists, bioinformaticians, biologists and software developers to conceive, implement, and execute innovative data analysis methods.

This is a challenging assignment with a motivated team in a high-paced, entrepreneurial work environment coupled with excellent opportunities for career development in a leading multinational corporation.

Qualifications

REQUIRED:

  • PhD in Computational Biology, Systems Biology, Computational Genetics or a related field with >5 years relevant work experience, MS with >8 years of experience or BS with >10 years of experience
  • 2 years in a leadership role with direct reports
  • Proficient scientific programming/scripting in R, ASReml, SAS, Python, C, Perl, or other relevant languages. Ability to work in UNIX computing environment.
  • Understanding of Deep Learning, advanced Machine Learning, and statistical methods applied to integrated analysis of biological datasets (e.g. association genetics, mixed model approaches, machine learning algorithms, data integration, meta-data analysis, network analysis, etc.)
  • Excellent organizational, communication and project management skills
  • Display curiosity and demonstrate the ability to quickly learn new scientific areas.
  • Must be goal oriented, customer focused and able to work in a fast-paced international team setting

PREFERRED:

  • PhD in Computational Biology, Systems Biology, Computational Genetics or a related field with at least 5 years of industry or academic experience
  • Experience using Deep Learning and advanced Machine Learning to solve complex biological questions
  • Experience working in an industry or academic environment for 5 to 10 years
  • Experience with model plant, crop, and microbial data sets

Scoping Questions

    Required:
  1. Do you have a PhD in Computational Biology, Systems Biology, Computational Genetics or a related field with >5 years relevant work experience, MS with >8 years of experience or BS with >10 years of experience?
  2. Do you have at least 2 years in a leadership role with direct reports?
  3. Are you familiar with Deep Learning and Machine Learning and how they can be applied to address biological questions?
  4. Are you proficient in scientific programming/scripting in R, ASReml, SAS, Python, C, Perl, or other relevant languages?
    Preferred:
  1. Do you have a PhD in Computational Biology, Systems Biology, Computational Genetics or a related field with >5 years of industry or academic experience?
  2. Do you have experience with model plant, crop, or microbial computational biology?

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