[DL] PhD Scholarship Opportunity on Visualisation of Expressive Ontologies at Monash University, Australia

liyuanfang at gmail.com liyuanfang at gmail.com
Mon Apr 27 03:53:20 CEST 2015

*** Apologies for cross posting. ***

==PhD Scholarship Opportunity on Visualisation of Expressive Ontologies at Monash University, Australia==

===The Opportunity===

Applications are invited for a funded PhD scholarship position at Monash University, Australia. The successful candidate will perform research in the junction of information visualisation, bioinformatics, and the Semantic Web. The candidate will work under the supervision of Prof. Falk Schreiber and Dr. Yuan-Fang Li at the Faculty of Information Technology, Monash University.

The Gene Ontology (GO) [1] is one of the most widely used biomedical ontologies. It comprehensively describes different aspects of genes and gene products under three broad categories, (1) biological process, (2) cellular components and (3) molecular functions. GO is currently being actively extended in the LEGO project to create a new annotation system to provide more extensible and expressive annotations.

This project aims to investigating novel visualisation techniques for GO-LEGO and its integration with the Systems Biology Graphical Notation (SBGN) [2]. The information can be seen as networks, and although there are some solutions for network layout, none is particularly tailered towards this application. Specifically we will investigate how domain knowledge captured in ontologies can assist in creating high-quality layouts.

[1] Ashburner, Michael, et al. "Gene Ontology: tool for the unification of biology."Nature Genetics 25.1 (2000): 25-29.

[2] Le Novère et al. "The Systems Biology Graphical Notation" Nature Biotechnology 27 (2009): 735-741.

===Candidate Requirements===

The successful student will have an excellent academic track record in computer science, bioinformatics or a related discipline. Applicants are expected to possess very good programming and analytical skills, be able to work independently as well as cooperatively with others. Research experiences in ontologies, knowledge representation, bioinformatics or information visualisation would be highly advantageous.

Candidates will be required to meet Monash entry requirements which include English-language skills. Details of eligibility requirements to undertake a PhD are available at http://www.monash.edu/migr/apply/eligibility/phd/ and http://infotech.monash.edu/research/degrees/prospective-students/entry-requirements.html.


The scholarship will be awarded at the equivalent of Australian Postgraduate Award (APA) rate, which is currently $25,392 per annum full-time (tax-free). The scholarship is tenable for three years, and extendable for up four years, dependent on satisfactory progress and availability of funding.

===Organisational context===

Monash is a university of transformation, progress and optimism. Our people are our most valued asset, with our academics among the best in the world and our professional staff revolutionising the way we operate as an organisation. For more information about our University and our exciting future, please visit http://www.monash.edu.

The Faculty of Information Technology (http://www.monash.edu/infotech) undertakes teaching and research across a broad range of information technology disciplines: computer science, computational science, intelligent systems, software engineering, network computing, information systems, business intelligence and decision support, multimedia computing and applications, information management, and knowledge management.

It is one of the few faculties of information technology in the world and one of the largest academic information technology units within a tertiary institution in the world. Its research-intensive, multidisciplinary, international capabilities provide it with a set of exciting teaching, research, and engagement opportunities that position it uniquely within the tertiary sector.

The Faculty has a strong commitment to providing the highest-quality learning opportunities for its students. The Faculty's research degrees are designed to produce high-calibre scholars who are capable of cutting-edge pure or applied research in either academe or practice.

The Faculty strives to undertake high-quality, high-impact research. It has chosen to focus its efforts through four research flagship programs, namely:

  * Computational Biology
  * Data Systems and Cybersecurity
  * IT for Resilient Communities
  * Machine Learning
  * Modelling, Optimisation & Visualisation

These flagships provide a highly focused research direction in particular areas where the Faculty has significant and internationally recognised research expertise. In addition, they inform the teaching activities of the Faculty.

===Submitting an Expression of Interest (EOI)===

Interested applicants should submit the following:

  * The expression of interest (EOI) form (http://www.infotech.monash.edu.au/research/degrees/prospective-students/fit-expression-of-interest.doc) required by Monash University,
  * A resume in PDF containing tertiary academic track record and achievements, research and work experiences (if any), and contact details of 3 referees,
  * Academic transcripts, and
  * A brief statement explaining your motivation and suitability for undertaking PhD research on this topic.


For more details about the project and the scholarship please contact:

  * Prof. Falk Schreiber (falk.schreiber at monash.edu)
  * Dr. Yuan-Fang Li (yuanfang.li at monash.edu.)

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