Newsletter 3 - The future sometime

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University-wide Academic Calendar.

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This Term

For the Bioinformaticians (To be shared with Line managers and Mentors).

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1 - Understanding the Bioinformatics Workplace:

The Bioinformatics work environment provides a rich setting for exploration and discovery of a range of knowledge, skills and understanding. This module enables students to have the opportunity to deepen their understanding of their specific work environment, by undertaking an enquiry using self-directed learning. Three strands formulate an integrated approach to this module: Learning about work - relates to developing the students’ knowledge and understanding of their workplace; Learning through work - examines the acquisition of practical skills in their real working environment; Learning for work - allows the students’ knowledge and skills to develop in a way that is directly relevant to the workplace. Making strategic decisions, quality issues and control are all part of the workplace, as is mapping business needs and delivering technology. The module enables students to reflect on their own work practice, critically appraise their own performance and report on the experience of learning at work, utilizing higher-order evaluative and analytical skills. Preparation: students will agree a topic related to their work practice with their module tutor and produce a proposal on what they plan to do. The project will be negotiated on a student-by-student basis and may include mentoring by work-based supervisors who will assist in the choice of subject on which the student will undertake an enquiry. Students will be required to submit an enquiry proposal, including a rationale, showing that they have made informed decisions about their intended topic. Implementation: Students will develop and maintain a reflective learning log as part of their ePortfolio, to be used as the basis of tutorial work and formative assessment to support this module and their continuing studies. They will participate in facilitated online discussions and Wiki activities, including peer assessment. Students will be encouraged to consider a diversity of learning strategies and to be imaginative in their proposed assessment vehicle(s). The final submission will include the ePortfolio. Students will be expected to demonstrate skills in information gathering, research and analysis, and an awareness of ethical issues relevant to their practice and studies. Successful completion of this module will demonstrate, amongst other qualities, the ability to self-evaluate, to self-manage, and to respond constructively to guidance; all qualities much valued by modern employers.

Goals include:

The student will be tasked with identifying the following aspects of the work setting:

The work environment (e.g. physical, social, hierarchical)

Business structures and pipelines

Health, safety and well-being of the work environment

Maintenance of professional and ethical standards

Organisational culture and goals

Evaluation of professional/occupational practice/procedures

Effective team working

Communication in the work place - between workers, stakeholders and customers / clients

The student will develop the following skills:

Generic and transferable workplace skills

Developing reflective practice, with self-assessment of skills, understanding and attributes for the work sector and learning

Managing own time and resources

Investigative skills and techniques Effective communication - description, discussion, evaluation and analysis

Introduction to personal development and planning mentoring

Proposal formulation, project planning and management

The nature of learning outcomes and of appropriate assessment method(s)

Analyse the relationship between theoretical perspectives, and workbased and key transferable skills required to support learning in the workplace.

Critically analyse a business domain; highlight issues and identify opportunities for improvement through evaluating systems in relation to their intended purpose and effectiveness.

Negotiate, plan and carry out an appropriate study in a work-related context, reflecting on and analysing the relationship between organisational culture and goals and specific practice.

Present, using appropriate technology, an evaluative account of their learning.

Assessed by:

Coursework 40% weight

Enquiry Proposal

Coursework 60% weight

Project including ePortfolio

Book list:

Experience at your Job by You

Recommended Time Allowance:

150 Hours for the Term

12.5 Hours per Week

Minimum Time Allowance:

36 Hours for the Term

3 Hours Per Week

This does not include time required for coursework.

2 - Databases, Management and Analytics

Databases are used to store and process data. Data are accessible through various interfaces such as web pages, APIs (Application Programming Interface), or SPARQL (SPARQL Protocol and RDF Query Language) endpoints. In this module, students will explore the main databases available for the different types of biological entities (DNA, genomes, RNA and proteins), the databases representing biological concepts (e.g. cladistics, taxonomy and ontology), and other biological databases, including those covering gene expression, protein-protein interactions and orthologues. Students will learn how to find resources, and how to design and perform a query to retrieve specific data. They will apply this knowledge in order to cross-link data from different databases. Students will also learn how to perform statistical analysis to evaluate retrieved data. In this module, students will learn about the key features of different database systems and consider cases where these different features are useful. Focusing on a relational database, students will explore the possibilities and the limitations of such database management systems (DBMSs). In medical science, databases contain patient personal information. Students will be introduced to the ethics of data usage and constraints surrounding such sensitive data.

Goals include:

Major bioinformatics databases - knowing their categories and understanding their interfaces

Relationship (cross-linking) between databases

Different types of database systems, and usage of RDBMS in particular

Formulate a query and determine the appropriate database in which to apply the query, with regard to the elements available (e.g. sequences, identifiers, gene/protein/molecule name) and the biological question at hand.

Design a basic relational database schema in order to store complex biological entities and develop quality checks for data integrity according to the data model in question.

Run a query, obtain and parse results, and carry out statistical analysis on datasets to evaluate relevance and quality.

Store the results in a relational database, in a program-accessible manner.

Assessed By:

Coursework - 60% weight Exam - 40% weight

Book list:

Not Released

Recommended Time Allowance:

150 Hours for the Term

12.5 Hours per Week

Minimum Time Allowance:

36 Hours for the Term

3 Hours Per Week

As we know however there is already more than 3 hours of preparation for the week as it is.

This also does not include time required for coursework.