Hackathon 2024

Biology Meets Big Data
hackathon
Published

June 12, 2024

Biology Meets Big Data Hackathon 2024

Welcome to the University of Glasgow Computational Biology Hackathon. 

Are you passionate about unravelling the mysteries of life through code and data? Do you dream of collaborating with brilliant minds to tackle complex biological problems? Look no further! Our exclusive hackathon is designed for researchers, students, and enthusiasts who share a common goal: advancing computational biology.

Sign Up Here!

Event Details

  • Date: 12th-14th June, 2024

  • Time: 10am-4pm

  • Location: McMillan Round Reading Room, Main Campus, University Avenue.

Why Participate?

  1. Interdisciplinary Exploration: Dive into the intersection of biology, computer science, and big data analysis.

  2. Networking: Connect with fellow researchers and forge collaborative relationships across the University.

  3. Challenging Problems: We have curated an exciting range of projects with associated data. Choose your challenge!

  4. Skill Enhancement: Learn new coding and data handling skills.

Who Should Attend?

  • Postgrads: Whether you’re a Masters or a PhD candidate, this hackathon is your chance to apply computational techniques to real-world biological questions.

  • Researchers: Join forces with fellow scientists to crack complex problems. Collaborate, brainstorm, and innovate!

  • PIs: Share your expertise and mentor the next generation of computational biologists.

The Projects

  1. Development of a compact and concurrently accessible open-source standard file format for pyramidal whole slide pathology Images to facilitate AI training.

Project lead: Chris Walsh (c.walsh@crukscotlandinstitute.ac.uk)

Advances in digital pathology have revolutionised the field but resulted has in the challenge of managing vast amounts of data. However, whole slide imaging scanners output the data in proprietary formats which often lack accessibility and flexibility. To address the issue here we propose building a new open source pyramidal file format.

More information about this project can be found here.

  1. HGP-LASAGNE: Resolving histopathological growth patterns in colorectal–liver metastasis into layers of spatial heterogeneity

Project lead: Tengyu Zhang (t.zhang.6@research.gla.ac.uk)

Colorectal cancer (CRC) represents a significant global health challenge, ranking as the second-leading cause of cancer-related deaths worldwide. There is a critical need to understand the metastatic processes and imaging based spatial transcriptomics offers this unique opportunity. The goal of the hackathon is to analyse unpublished spatial transcriptomics data from Jamieson Spatial Lab.

More information about this project can be found here.

Please note that you will have to sign a data sharing/protection declaration before starting work on this project.

  1. Host-Pathogen Extractor: Using text mining, Natural Language Processing, and Deep Learning to automate database creation for infectious disease research and surveillance

Project Lead: Max Farrel (maxwell.farrell@glasgow.ac.uk)

Large scale databases of host-pathogen interactions underlie models that predict future emerging infectious disease threats, and guide surveillance of cross-species pathogens. As the number of papers increases exponentially, automated ways of extracting this information should be considered, however those have been rare in ecology. As part of this project, the hackathon teams will explore different ways of extracting host-pathogen interactions from abstracts, from traditional pattern matching to applying large language models.

More information about this project can be found here.

  1. The FAIR Data Pipeline: Provenance driven data management

Project lead: Ryan Field (ryan.field@glasgow.ac.uk)

To address the issues of FAIR and traceable data and models, the FAIR data pipeline was developed. It is available for various programming languages and is continuously developed by a very small team. The project would greatly benefit from further testing, bug fixing and tutorials. During the Hackathon we hope that team members can test the pipeline on their own real world data and help improve the user experience and documentation.

More information about this project can be found here.

  1. Development of an iCLIP2 data analysis tool, mapping protein footprints on RNA.

Project lead: Rozeena Arif r.arif.1@research.gla.ac.uk

Project Summary: Protein-RNA interactions play a vital role in virus-host infections. It thus becomes essential to identify the binding interfaces between these two molecules for efficient understanding and manipulation of the mechanism. CLIP experiments provide highly precise binding sites during interaction. Analysis of such data is a complex, multistep and attention demanding process. We propose to build a pipeline to automate the analysis steps considering specific conditions of an experiment.

More information about this project can be found here

FAQs

Q1: I want to participate but worried about my coding skills/AI knowledge/etc?

A1: Hackathons are a great environment to learn, so don’t worry, just be upfront with your team lead. You can still contribute in so many ways, like ideas, writing, biological knowledge, management, etc.

Q2: I can only attend 2 out of the 3 days. Is this a problem?

A2: While attending the full duration of the Hackathon would be beneficial, we understand that committing 3 days might be difficult for some. Please include that information in your application form.

Q3: I am a master student and worried about my skills suitability.

A3: See Q1. We welcome participants from diverse backgrounds and you can contribute in many different ways. Also, please note that most projects require initial preparation before the Hackathon.

Q4: What if I don’t know any other participants?

A4: This is a great opportunity to get to know people from across the university! You don’t need to have spoken to anyone prior to signing up, just fill out the sign-up form and you will be made very welcome.

Q5: Will I definitely be included in the team for my preferred project?

A5: We aim to offer every participant a spot on their preferred team but this may not be possible if a project is oversubscribed. This is why we ask you to rank projects by preference on the sign-up form. If there is a project you don’t want to be considered for, please indicate this on the form.

Registration

Ready to embark on this scientific adventure? Pick your preferred project and reserve your spot now. Limited slots available! Please express your interest and fill in the form by the 31st of May.