Available Positions

The Ideker Laboratory is in continual open recruitment for excellent postdoctoral scholars, graduate students, and software engineers. To apply, please send a current CV and references to Dr. Trey Ideker (tideker@ucsd.edu).

PhD Students

Prof. Ideker receives a large volume of emails asking about how to join the Ideker Lab. If you are a student who wants to be admitted to UCSD graduate programs, please directly check out the website of the BISB, BMS, Bioengineering, or CS programs. If you've already been admitted to a UCSD PhD program, please do the following before contacting Prof. Ideker: please watch Prof. Ideker's talk at AACR 2018 , read our Research page, and read some of our papers on the projects that interest you.

Postdoctoral Fellows

We are recruiting bioinformatics postdocs and senior research scientists to three recently funded NIH cell mapping centers: the Cancer Cell Map Initiative (CCMI), the Psychiatric Cell Map Initiative (PCMI) and the Host Pathogen Map Initiative (HPMI). The goal of these positions is to use data generated by the centers to develop advanced computational models of cell biology for use in translating patient data to successful therapies. Currently, there is much interest in building intelligent systems for this purpose, under the banner of precision medicine. However, the current machine learning models face particular challenges when applied to biology, including handling of extreme data heterogeneity and lack of mechanistic insight into predictions. The premise of the CCMI, PCMI and HPMI is to address these challenges by building machine learning systems that are trained to learn not only biological function but also biological structure. Further vision and details for this research are described in this Perspective article in Cell. Applicants must have a PhD in bioinformatics, computer science or a related discipline, a strong background in machine learning and bioinformatics, and a history of productive publication.

Software Engineers

We are currently recruiting for two open positions: Cytoscape Cyberinfrastructure Programmer and System Administrator and Project Coordinator

Cytoscape Cyberinfrastructure Programmer

For more information and to apply, please go to: https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=96165

The Cytoscape Cyberinfrastructure  Programmer will assist in creating and maintaining elements of the Cytoscape and NDEx, work flexibly across multiple technologies (both front-end, back-end, and database), and acquire skills in new programming languages and environments, packages, and databases. Also, under supervision, the Programmer will assist in maintenance and development of existing code bases, including Cytoscape and its apps.

Other responsibilities will be to assist in system administration of public and internal servers. Software deployment and distribution and assist in database management, backup, migration, and recovery.

The CI Programmer will interface with colleagues from project sponsors, and with collaborators in the UCSD community and worldwide.

MINIMUM QUALIFICATIONS

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

A minimum of two (2+) or more years of programming experience.

Knowledge of secure software development. Working knowledge of software engineering, applications programming and web development.

Demonstrated experience with common programming tools. Demonstrated ability to follow software specifications.

Intermediate skills associated with the design, development, modification and deployment of software, including object-oriented programming concepts.

Demonstrated knowledge of other IT related areas. Knowledge of bioinformatics methods and data structures.

Strong software repository skills. Experience with development in Java, Javascript/HTML5, Python or R, web application frameworks, object-orientation, documentation, unit testing, and releasing software.

Ability to work in a Unix, Windows and Mac environments.

Working knowledge of databases. Proven ability to organize large volumes of data using creative tools, logs and databases created to use with multiple research projects.

Outstanding writing and editing skills using knowledge of conventions of academic style, English grammar, punctuation, and spelling. Ability to re-write text that is ambiguous, unorganized or grammatically incorrect.

Effective communication and interpersonal skills. Ability to communicate technical information to technical and non-technical personnel at various levels in the organization.

Strong interpersonal and communication skills, including tact, diplomacy, and flexibility. Ability to communicate clearly and concisely, verbally and in writing. Ability to work successfully with a diverse group of people with varying perspectives and needs.

Proven problem-solving skills. Strong decision making skills and ability to use independent judgment and discretion to quickly set priorities and establish new procedures when needed.

Ability to research, analyze, recommend, communicate, and implement solutions. Ability to function successfully with minimal direction. Self-motivated and works independently and as part of a team. Able to learn effectively and meet deadlines.

Demonstrated ability to maintain strict confidentiality.

PREFERRED QUALIFICATIONS

Prior experience working in an environment where research relates to human diseases and developmental processes.

Demonstrated ability to interpret/coordinate research protocols and the corresponding data requirements.

Experience with the design, development, and maintenance of data collections used for data storage and analysis in a biomedical research environment.


System Administrator and Project Coordinator

For more information and to apply, please go to: https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=95903

The UCSD School of Medicine is involved in development of several bioinformatic resources for network analysis that are widely used by the biological research community. The best known is Cytoscape (http://www.cytoscape.org), a collaborative open-source software project. Cytoscape is a leading workstation-based platform for visualizing and processing complex networks. It is widely used with approximately 17,000 downloads per month. NDEx, the Network Data Exchange (http://ndexbio.org), is another major project, a public web resource for sharing, storing, accessing, and publishing biological knowledge as computable networks.

The System Administrator and Project Coordinator (SAPC) will manage, maintain and extend the computing infrastructure, both hardware and software, and they will support the users of that infrastructure. The System Administrator and Project Coordinator (SAPC) will work with the software development team to deploy and administrate cloud hosted websites and services, including usage analysis and reporting. Finally, the SAPC will coordinate the software release process for the web and desktop products of the software development team, including the management of issue tracking and user bug reporting.

Lab infrastructure system administration: The SAPC will administrate scientific computing infrastructure that includes the secure compute clusters, a VM cluster, a GPU server, lab workstations and compute servers, and multiple storage servers. Most of the systems are housed at the San Diego Supercomputing Center (SDSC). Administration will include maintenance of the rack-mounted systems at SDSC, diagnosing hardware problems, replacing components and installing new systems.

The SAPC will work with stakeholders to design hardware and software solutions as the infrastructure evolves to meet new demands. Will manage the purchasing process and interface with vendors for warranty support. They will monitor alerts and performance metrics and will plan and manage data and image backup. They will manage the user authentication system, gateway computers, the firewall, VPN, samba server, IP allocation and Hostmaint. They will control the configuration of all systems, using tools such as Puppet. The SAPC will also maintain the documentation for the systems, including hardware configuration.

Lab user support: The SAPC will install and maintain user workstations and other computers onsite. They will control the software configuration of these systems, including the installation of commonly used packages. They will diagnose problems and install and replace hardware. They will assist lab members in the configuration of personal machines for interfacing to the lab infrastructure. They will maintain and extend user documentation for lab computing.

The SAPC will assist in the IT issues encountered when installing or maintaining scientific instruments in the wet lab, including interfacing with vendors for support and managing regular backups of attached computers. The SAPC will manage user accounts and commercial software used in the lab. They will monitor the usage of the lab computing infrastructure and assist users in using those systems, answering questions, fielding bug reports and otherwise responding to requests.

Cloud website and service system administration: The SAPC will administrate websites and web services hosted on cloud providers including AWS and Google. They will track usage of these systems, using both standard tools and custom logging and reporting systems. They will prepare periodic reports of usage, working with the software development team to plan and implement appropriate metrics. They will perform backups, respond to outages, and work with the software development team to make the deployed systems robust and secure.

Coordination of software release process and issue tracking: The SAPC will work with the software development team to maintain and administrate internal issue tracking systems and end-user bug and issue reporting systems. They will manage aspects of the software release process, including maintaining schedules, organizing and tracking testing, and performing final deployment to the web.