Positions Available

Post-docs:

The LemBix Lab is interested in recruiting post-docs with expertise in bioinformatics, biochemistry, molecular biology, and cell biology.  A background in neuroscience is helpful but strong evidence of productivity and publications is even better.  A willingness and ability  to work on team-based projects is required.  Send a copy of your C.V. and a statement of your interests to either Dr. Lemmon or Dr. Bixby.

Description of BioAssay Ontology (BAO) Project

One of the components of the NIH Roadmap for Medical Research involves high-throughput screening and the development of small molecule chemical probe (tool) compounds.  Recently, this initiative has been producing massive amounts of small molecule bioactivity data, which are publically available in PubChem and other databases.

We are developing a BAO and software tools to formalize the domain of biological (high-throughput) screening assays with the goal of facilitating large-scale analyses of the growing body of diverse data sets, its integration with other life science databases, and ultimately to enable biomedical knowledge discovery.

For this project we are looking for talented and highly motivated individuals with expertise in biological high-throughput and / or high-content assay technologies and assay design.  The work will involve curation, annotation, organization, analysis of screening data and other aspects of systematic content development. The positions offer an introduction to the rapidly growing field of knowledge engineering and the opportunity to work with various industry standard tools.  The positions are integrated with other components of the project such as ontology engineering, software engineering, data integration and visualization.  This is a visible multidisciplinary project and the positions require good communication and collaborative skills.  Its successful execution can have a large impact on academic and pharmaceutical biomedical research.  Biological data curation, integration and knowledge engineering has become an essential part of biomedical research and discovery.  The positions are therefore suitable to prepare for an academic as well as industrial career.

Contact Stephan Schürer, sschurer@med.miami.edu or Vance Lemmon, vlemmon@miami.edu

We are seeking: 

Scientific Software Engineer:

Description of the Position
This position primarily involves software engineering, but requires close collaboration with an ontology developers and content curators.  The Scientific Software Engineer will develop user-friendly software tools to facilitate the productive development and integration into chemical biology workflows of BAO and BAO-annotated data sets.  Software is needed for experimental data- and ontology-ontology mapping and standardization, integration of orthogonal data types (via BAO), and applications to browse and search domain-specific databases via BAO.  Responsibilities also include development and end-user documentation.

Requirements
M.S. in computer science, bioinformatics, or a related field with significant software engineering experience.  This position requires demonstrated experience in efficiently developing and integrating software solutions with a record of prior accomplishments.  Experience in developing software solutions involving the integration of diverse data types and knowledge extraction by software agents utilizing ontologies is specifically preferred.  In particular we prefer experience with technologies such as Jena, Sesame, SPARQL to manage, query, integrate diverse data by use of ontologies.  Knowledge of ontology development and practices (specifically in a computer science and information science context) and ontology representations (such as OWL) and ontology browsers is desirable.  Basic knowledge of bioinformatics including representations of biological entities and pathways and pathway databases (such as PID and KEGG) is desirable.  Knowledge of PubChem, PUG, the PubChem XML schema and representations of chemical structures is desirable.  Technical skills should include Java and rapid development frameworks, Hibernate, MySQL, Sping, and Dojo.  Experience in GUI design and development using prototyping tools such as Caretta is also desired.
The position requires the ability and desire to work in a multi-disciplinary team in close collaboration with software engineering, computer science, ontology engineering, content development, cheminformatics, and to adapt to a highly collaborative and interdisciplinary work environment.

Scientific Content Curator:

Description of the Position
In this position your primary responsibility is to categorize and annotate screening experiments and end points in the context of the Bioassay Ontology.  With your HTS and / or chemical biology expertise you will also contribute to the development of the ontology and contribute to the specification and testing of software tools to query the annotated database.  This work also involves extracting and developing standardized vocabularies, synonyms and concepts to describe biological assays and capturing these terms and their organization using software tools.  It also requires the standardization and reorganization of various end points in screening databases to facilitate their global comparison.  It is expected that you develop skills of ontology and knowledge engineering.  Further responsibilities involve developing end user requirements for software tools and documentation.

Requirements
M.S. and 3 years experience in biochemistry, cell biology, pharmacology, bioinformatics or a related field. A working knowledge with PubChem and other chemical biology databases (such as ChemBank, PDSP, Binding DB) is desired.  Experience with pathway databases (such as KEGG, PID) is desired.  Knowledge of ontologies in biology and their purpose, in particular Gene Ontology (GO), and their application is desired. Experience with representations and languages to describe biological entities, pathways and their interactions is preferred.

The primary responsibility of the Scientific Content Curator is to categorize and annotate screening experiments and end points in the context of the BAO while contributing to the development of the ontology and software tools to query the annotated database.  This work also involves extracting and developing standardized vocabularies, synonyms and concepts to describe biological assays and capturing these terms and their organization using software tools.  It also requires the standardization and reorganization of various end points in screening databases to facilitate their global comparison.  Further responsibilities involve developing end user requirements for software tools and documentation.

Bioassay Knowledge Engineer:

The primary responsibility of the Bioassay Knowledge Engineer is to develop and design the concepts, objects, properties, and relationships that are required in BAO.  This involves the development of standardized vocabularies, extraction of terms and synonyms and their logical and clear conceptualization using ontology engineering principles.  It also requires the extraction and curation of assay content and end points from databases such as PubChem.  This position will also be involved with developing end user requirements of the ontology and documentation.