Job# CR/16095/WCS
Bioinformatics DBMS Implementor Job Opening

Computational Research Division
High Performance Computing Research Department
Scientific Data Management Group

Lawrence Berkeley National Laboratory
Berkeley, California
United States

KEY SKILLS DESIRED

ML, Java or C++, DBMS use and implementation, significant implementation experience, visual languages, graph algorithms

POSITION SUMMARY

Under the direction of the Graph Data Management project leader, this programmer will assist in the implementation of a general purpose graph data management system, which will be used to store a variety of chemical reaction system descriptions, e.g., biopathways (metabolic and signaling pathways, genetic regulatory networks) and protein interaction networks data for the BioSPICE and Genomes to Life projects at Lawrence Berkeley and Sandia National Laboratories. The project involves specification of graph data model, a graph query language (including recursive path queries, shortest path queries, subgraph isomorphism and subgraph homorphism queries, graph difference, largest common subgraph, etc.), query API, visual query interface (based on graphs), query language parser, query optimization, query execution system, interfacing to a backend relational DBMS, data exchange formats, and some federated database management of experimental datasets stored in other relational databases. We are planning on implementing the project partially in a functional programming language (e.g., ML or CAML) for the query parser and optimizer (and possibly query execution), and partially in Java for the user interface code and partially in C/C++ for the graph algorithm library. The external query API will probably be in SOAP, with data exchange in XML.

See the URL: http://pueblo.lbl.gov/~olken/graphdm/graphdm.htm for a more detailed description of the project.

DUTIES

ESSENTIAL -- Programming, debugging, testing, and documentation of the visual graph-based query interface, query API, query language parser, query optimizer, query execution engine, graph algorithms, interface to backend relations DBMS, data import / export. Assist in the design of the graph data model, graph query language, optimizer, query execution engine, graph algorithms, data exchange formats. MARGINAL -- Writing papers describing project for publication. Conducting demonstrations and training in use of software.

QUALIFICATIONS

ESSENTIAL -- Demonstrated ability to develop, test, maintain and document substantial software projects in Java, C++, or a functional programming language such as Haskell, ML, CAML, Scheme or Lisp with limited supervision. Experience with database management systems, either relational, object oriented, or XML. Ability to conduct effective technical communications in English, both oral and written. Ability to work in a team setting. B.S. in Computer Science, Information Systems, Bioinformatics, or related field or equivalent experience. MARGINAL -- Familiarity with Unix/Linux; design and implementation of visual languages (e.g., visual programming or query languages); graph algorithms; graph theory; knowledge representation (e.g., OWL, RDF or DAML+OIL); relational database management systems administration, implementation and use; query optimization; recursive query processing; conceptual graph systems; functional programming (e.g., Haskell, ML, CAML, Scheme, or Lisp); graph grammars; chemoinformatics; SOAP; XML schemas; XML query languages; XML parsing and generation; graph drawing algorithms; visual programming interface design and implementation. Knowledge of molecular biology or biochemistry. Experience in conducting software training. M.S. or Ph.D. in Computer Science, Information Systems, Bioinformatics or related field or equivalent experience.

POSTING DATE: June 5, 2003 CLOSING DATE: Open until filled.

NOTE(S)

This is a one-year term appointment with the possibility of renewal.

Employment at LBNL does NOT require U.S. citizenship.

Berkeley Lab is an AA/EEO employer.

TO APPLY

If you would like to forward your resume for consideration, select one of the following methods: In your cover letter, be sure to reference job title and source code CR/16095.

On-line URL: http://cjo.lbl.gov.
Use our on-line format in Current Job Opportunities.

E-mail to: CSRecruiter@lbl.gov.
Send your cover letter and resume in plain text. No attachments please.

RELATED URLs

LBNL Computing Sciences Employment Opportunities URL: http://www.lbl.gov/CS/Careers/OpenPositions/index.html

Additional job opportunities at LBNL can be found at the LBNL Current Job Opportunities website at the URL: http://cjo.lbl.gov.

LBNL Human Resources URL: http://www.lbl.gov/Workplace/HumanResources/

Lawerence Berkeley National Laboratory URL: http://www.lbl.gov/

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This work sponsored by the Department of Energy OBER/MICS offices
Last Modified July 27, 2003 by Al Geist