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Bioinformatics Service Requests

Introduction

The Division of Computational Biology (CBIO) at UCT provides bioinformatics support to researchers at the University of Cape Town. Two dedicated bioinformaticians were recently appointed: Dr Katie Lennard as lead bioinformatician for the Institute of Infectious Disease and Molecular Medicine (IDM) and Dr Jon Ambler as lead bioinformatician for the Clinical Infectious Diseases Research Initiative (CIDRI). Although requests from the IDM and CIDRI therefore take priority, we welcome requests from other researchers and follow a collaborative model. That being said, we do not receive funding from UCT outside of IDM and CIDRI to provide support and we therefore encourage researchers to budget for bioinformatics services in their proposals.

We can assist in building bioinformatics pipelines and tools to use, as well as some basic training. We have a small computer cluster at CBIO and ICTS have a high performance compute cluster, both of which have several bioinformatics applications and pipelines installed. Members of UCT can apply for access to the ICTS cluster and they provide basic training on how to use the cluster and help with installation and use of new tools. Although our team has a wide range of skills, bioinformatics is a large area. If a support request is outside of our area of expertise, we’ll do our best to point you in the right direction as we have excellent relations with other South African bioinformatics groups. We recognise that there are a wide range of needs and we shall endeavour to be as flexible as possible. We emphasise the need to talk to us during the planning phase of your research project. Bioinformatics is a large component of many projects and must be planned from the beginning both with respect to scientific method and available resources.

Data Transfer and Storage

ICTS provides access to storage for UCT staff and students for a fee once you have exceeded your UCT member quota. You can contact eResearch directly to arrange this or we are happy to facilitate the engagement between researchers and ICTS to determine the appropriate size and access required. At CBIO we can provide access to temporary storage when you are transferring big files from external resources.
This must be moved within a few days to your dedicated storage area at ICTS. We can also help with the actual transfer. We use Globus online for big data transfers, which requires the data provider to have a Globus online instance too.

Consulting/Bioinformatics Analysis

Bioinformatics support is often in the form of technical support –writing scripts or setting up software or a whole pipeline. Do not underestimate the time required for someone to do this for you, as all software is different and no two analyses are identical. Scientific input is also frequently required in order to determine the best method to use, interpretation of the data, etc. Our staff usually have to put in time doing research on papers describing different methods and approaches.

This type of support can be split into three types:

1. Ad hoc requests: Much of our time goes into assisting with small requests: How do we install this software? How do we run that software? Why is my R script broken? Which bioinformatics technique is best for this type of data? Each project can be negotiated on a case‐by-case basis, but generally up to about 8 hours of work can be done without any cost (though we would appreciate acknowledgement on a dissertation or paper). Ad hoc requests will be handled on a case-by-case basis, with queries addressed either via email or alternatively during our open-door consulting hours (details below). Beyond this, we need to negotiate a more formal arrangement, as this requires a significant input of time from our staff who are employed on other projects. The focus of this type of service is to improve your capacity to help yourself.
2. Collaborative Model: Our preferred model for more extensive work is a collaborative model: we collaborate on your project and the person or persons on our staff who work with you become collaborators. Our role would be scientific and not entirely technical. Such collaboration should apply the ICMJE guidelines regarding authorship.
3. Service for payment: This is not a preferred option but we would consider it. Payment would be made against some Service Level Agreement, and we would negotiate a per hour or per project charge.

Requests for support should be submitted by completing a services request form. If possible, please submit requests during the planning stages of your project – this will allow us to start developing data analysis pipelines tailored to your needs while you generate the data. IDM bioinformatics support will follow a collaborative model where our role would be scientific and not purely technical. Such collaboration should apply the ICMJE guidelines regarding authorship. A memorandum of understanding (MoU) should also be completed for collaborative projects.

Bioinformatics support members

Dr Katie Lennard
Affiliation: IDM primary Bioinformatician
Email address: katieviljoen@gmail.com
Open-door consulting hours: Wednesday morning between 9:30am and 12:30pm
Location: Room N1.06

Dr Jon Ambler
Affiliation: Bioinformatician at CIDRI-Africa
Email address: jon.ambler@uct.ac.za
Open-door consulting hours: Tuesday afternoon between 13:30 and 16:30
Location: Room N1.06.3