Post Doctoral Associate - BioAssay Knowledge Engineer
Posted November 2009
The Miami Project to Cure Paralysis and the Center for Computational Science (CCS) are developing a BioAssay Ontology (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.
We are looking for a highly motivated Post Doctoral candidate with expertise in biological high-throughput and high-content assay technologies and assay design, curation of biological screening data and content development, ontology engineering, software engineering and integration. This project is highly visible and collaborative. Its successful execution can have a major impact on academic and pharmaceutical biomedical research. It is therefore suitable as preparation for an academic as well as industrial career.
The primary responsibility 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 ontological 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. A PhD in biochemistry, cell biology, pharmacology, bioinformatics or a related field is required. This position requires expertise and detailed understanding of a wide variety of biological assay technologies and assay designs including biochemical assays, cell-based assays, high-throughput screening technologies, high-content imaging with detailed knowledge of the various common assay formats. Also required is the ability to conceptualize this knowledge and model it into a formalized representation. A working knowledge of PubChem and other chemical biology databases is required; knowledge of PUG and the Pubchem xml schema is preferred. Experience with pathway databases is required. Knowledge of ontologies in biology and their purpose in particular GO and their application as well as knowledge of ontologies in information science and computer science is preferred. Prior experience in the construction of ontologies and general ontology engineering principles is preferred.
Post Doctoral Associate - Scientific Software Engineer
Position No. 39991
Posted October 2009
The Miami Project to Cure Paralysis and the Center for Computational Science (CCS) are developing a BioAssay Ontology (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. 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.
We are looking for a talented and highly motivated post doctoral candidate with expertise in biological high-throughput and high-content assay technologies and assay design, curation of biological screening data and content development, ontology engineering, software engineering and integration. This position primarily involves software engineering, but requires close collaboration with an ontology developer and content curator. This project is highly visible and collaborative. Its successful execution can have a major impact on academic and pharmaceutical biomedical research. It is therefore suitable as preparation for an academic as well as industrial career.
The Post Doctoral Associate will develop user-friendly software tools to facilitate the productive development and integration into chemical biology workflows of BAO and BAO-annotated data sets. The candidate will also be responsible for development and end-user documentation. This position requires demonstrated experience in efficiently developing and integrating software solutions with a record of prior accomplishments. A PhD in computer science, bioinformatics, or a related field with significant software engineering experience and knowledge of small molecule biological screening is preferred. Experience in developing software solutions involving the integration of diverse data types and knowledge extraction by software agents utilizing ontologies is specifically preferred. 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 required. Basic knowledge of bioinformatics including representations of biological entities and pathways and pathway databases (such as PID and KEGG) is also needed. Specifically, technical skills must include Java and rapid development frameworks, Hibernate, MySQL, Sping, Dojo, and ideally the JChem technology.
Cheminformatics Post Doctoral Associate
Position No. 39509
Posted June 2009
The Computational Chemistry Program is looking for a highly motivated postdoctoral researcher interested in the development and application of chemical informatics and computational chemistry methods for the discovery of small molecule biological probes and drugs. This position provides the opportunity to work with an industry-standard chemical informatics and high-performance computing infrastructure and a wide variety of computational technologies in a multidisciplinary environment. This position includes research and collaborative drug discovery projects involving various cheminformatics, computational chemistry, bioinformatics technologies and in particular integrative approaches. This work is expected to lead to a number of publications. The position will prepare for an industry or academic career. Candidates for the position should hold a PhD in chemistry, cheminformatics, bioinformatics, computer sicence or other related field. A candidate with a chemistry background is preferred. Applicants are requested to apply through the UM Career site.
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