Internship Projects

The techniques currently used in the Technology Cores and the types of project they can support are summarised below. 

The actual projects offered or undertaken will be determined by a number of factors including, the applicants' interests and the type of projects available at the time of the internship. The details of potential projects will be shared with successful applicants before the start of the internship.

The bioinformatics core offers a 3-month internship for PhD students to enhance their bioinformatics skills through hands-on experience in research, software development, or education. Specialising in high throughput sequencing, the core supports projects involving genomic, transcriptomic, and proteomic data analysis. The internship will include training in bioinformatics applications and students will have access to advanced computational infrastructure. The core welcomes project proposals that fall within one of the following categories: 

Bioinformatics research and data analysis:

We are looking for students with innovative research questions who are eager to develop their bioinformatics skills or establish new bioinformatics methodologies. Candidates can propose projects based on their research or novel reanalysis of published datasets.

Bioinformatics software development:

Students interested in software development will have the chance to create robust pipelines or applications using platforms like Nextflow and Snakemake, potentially contributing to the broader bioinformatics community. Projects may involve designing new workflows or creating interactive web applications for data integration and analysis.

Bioinformatics education:

The core welcomes candidates interested in developing bioinformatics training materials or workshops. The team currently runs introductory courses in programming, statistics, and high-throughput sequencing analysis and seeks to expand into advanced areas such as single-cell sequencing, proteomics, machine learning, and long-read sequencing. Projects may involve developing new workshops or designing interactive methods for delivering courses.

The Light Microscopy Core (LMC) is an advanced microscopy facility equipped with a diverse array of microscopes, offering extensive scientific capabilities for a wide range of research needs. The LMC features laser scanning confocal microscopes capable of rapid imaging at sub-diffraction limits, achieving resolution down to 90 nm in live samples over extended time periods. This allows for detailed study of cellular dynamics and structural intricacies.

For delicate samples susceptible to phototoxic effects, the LMC provides spinning disk confocal microscopes. These instruments are both highly efficient and use minimal light exposure, ensuring the protection of sensitive specimens during imaging.

The facility also offers high-end widefield fluorescence microscopes, ideal for examining fluorescent protein intensity, distribution, and function in cell monolayers in both fixed and live specimens. To enhance data analysis, cutting-edge software tools are available for processing 2D and 3D images, with AI-driven solutions for particularly complex imaging challenges.

In addition, an optical tweezer system is available for single-molecule force measurements, enabling the study of molecular motors, DNA-binding proteins, and the conformational dynamics of protein and DNA folding.

The LMC is staffed by two full-time experts who provide specialized support in both image acquisition and analysis. Bespoke software scripting services are also available upon request to meet specific research needs. 

Several projects that take advantage of the LMC will be available, either in conjunction with one of the research groups in Edinburgh or related to your own PhD research. Please contact the LMC or the DRP academic leads if you would like to discuss ideas further.

The Discovery Research Platform for Hidden Cell Biology (DRP-HCB) Proteomics Core, specialises in bottom-up proteomics and uses a wide range of techniques to address important scientific questions. The Core is equipped with five state-to-the-art mass spectrometers, allowing us to offer a wide range of proteomic applications. 

We are very happy to support student internships focusing on improving our current methodology in sample preparation and instrument performance on protein quantification and post-translational modification (PTM) analysis. 

We can also provide support on cross-linking analyses of proteins and protein complexes with extensive training on our in-house cross-linking and visualisation software platforms. We are interested in evaluating Thermal Proteome Profiling (TPP) on various organisms and applying it on different instrumentation and we also aim to further improve high throughput analyses. 

We are also offering computer-based internships, in which, following training, we aim to evaluate various proteomic software platforms on a number of ongoing projects. Finally, we can support bioinformatic analyses on large scale proteomics datasets in order to answer project-specific questions. 

We provide a platform for discovering how proteins assemble into the molecular machines that underpin cell function.

The main approaches employed are:

• cryo-EM,
• X-ray crystallography,
• solution biophysics (including SAXS)
• structural modelling

We are particularly interested in developing approaches in which we combine data from different methodologies to build models of large macromolecular assemblies and we could support both laboratory-based and computational internship based projects.

Laboratory based projects

Developing methodologies in:

• single particle Cryo-Electron Microscopy (cryo-EM),
• Cryo-Electron Tomography  (cryo-ET) of protein assemblies and cellular structures,
• X-ray crystallography,
• Small-angle X-ray scattering (SAXS)

Computational projects

• In structural biology data integration,
• using experimental data in structural modelling, and in
• building accessible user interfaces to enable computational approaches to be adopted by a wider local user base.