Bioinformatics Service Requests
The Computational Biology Division (CBIO) at UCT is willing to play a role in providing bioinformatics support to researchers at the university. We can provide advice on bioinformatics protocols, methods and tools to use, as well as some basic training. We have a small computer cluster at CBIO and ICTS have a high performance computing cluster, both of which have several bioinformatics applicationsand 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. Like any service, bioinformatics services should be paid for. CBIO does not receive any UCT funding to provide support so there usually needs to be a quid pro quo for the support offered. 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 as early as possible in a 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 provide 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 outside.
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.
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 help: Much of our work is to help with small requests: How do we install this software? How do we run that software? 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 10 hours of work can be done without any cost (though we would appreciate acknowledgement on a dissertation or paper).
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.
Each project will be handled on its own merits, depending on the nature and size of the project. Small service requests can be handled informally (ad hoc help), while others will need more formal engagement to assess the best level of support we can offer. Please complete the questionnaire to engage with CBIO on providing assistance with your project.