NGSprint

Next year of NGSchool Society bring a new event - NGSprint!

It will be an online bioinformatics hackathon conducted by NGSchool members and friends, accompanied by a few lectures by renown researchers in the field. We will concentrate on various tasks around NGS data processing and analysis, as these were the topics most often mentioned in our recent survey. By the way, great thanks to all who gave us the few minutes and filled it!

Schedule

NGSprint will take place between 8^th and 15^th of September 2021. Below you can find tentative schedule. Please remember that it may change.

Topics

We are planning to form hackathon teams working on following topics:

1. RNAseq transcriptomics: from quality control to pathway analysis

• Anamaria Elek

• In this hackathon you will learn how to plan your RNA-seq experiments and analyze RNA-seq data. You will become familiar with important file formats and tools, and perform quality control, sequencing reads alignment, differential expression, functional enrichment and pathway analysis that will ultimately allow you to interpret your RNA-seq data. This hackathon is intended for people who are getting started with bioinformatics and/or this particular type of analysis.
• Requirements: being familiar with linux command line, R programming language and basic theoretical principles of RNA-seq.

2. Multi-omics data integration

• Karolina Sienkiewicz & Aakrosh Ratan

• Different experimental techniques (for example, RNAseq, DNA methylation profiling, or whole-genome sequencing) capture different cellular aspects of biological organisms. Effective integration of various omics data types allows us to observe effects that manifest at both genomic and epigenomic levels and provides us with system-level insights. During this hackathon, we will explore some frequently used methods for multi-omics data integration, including latent variable modeling and matrix factorization. The goal of the workshop is to provide an overview of models, their limitations, and some hands-on experience with integrative analyses using multiple data types.
• Requirements: familiarity with command-line and R programming language.

3. New generation of biomarkers: miRNA and machine learning models

• Urszula Smyczyńska & Szymon Grabia

• MicroRNAs (miRNA) are very promising biomarkers, but development of clinically useful tools requires careful experiment planning and considerable analytical effort. Starting from expression measurement technique through normalization to the model derivation and its validation, we make a lot of decisions that affect the final result. During this hackathon, you will have the opportunity to explore real miRNA expression data and make these choices consciously under the guidance of our mentors.
• Requirements: at least basic experience with Python.

4. Data visualization in bioinformatics

• Kasia Kędzierska

• A good figure can speak a thousand words while a less perfect one can confuse the reader instead of telling the stories. Learning how to visualise and represent complex ideas, especially large datasets such as the ones we tend to work on daily basis is crucial part of a bioinformatician's skill set. In this hackathon we will focus on telling stories with our plots. We will try to fix some confusing figures. We will also build our interactive graphs and animations, while also trying to understand when these are helping to convey the message and when they distract from the main points.
• Requirements: R (shiny not required but highly recommended), Python.

Each team will be working on one topic for about a week under the guidance of mentor(s). At the end of the event, all teams will present the result of their work.

The final list of hackathons will depend on other participants and their interest. It might happen that the hackathon you're most interested in will not be run. Then, we will then try to offer you the second best match. We will contact you when we close the form with results of the selection.

Stay tuned, more details coming soon!

Registration

Registration is required if you want to participate actively in the hackathon as a team member. Lectures will be open, available to wider audience and to watch them you don't need register.

Registration deadline: 24.07.2021 23:59 CET

Register

NGSprint FAQ

What is NGSprint?

NGSprint is a hackathon - an intensive collaborative problem-solving event - in which small teams (5-8 people) work on the analysis and interpretation of real-life bioinformatics datasets. Our hackathon will feature several topics, each of which will be moderated by dedicated mentor(s), and accompanied by lectures given by experts working in the related field.

How to get a place?

You need to carefully fill the registration form stating why you wish to participate in NGSprint. If there are more registrations than available places, we will select participants basing on your motivation

Is registration obligatory?

Registration is obligatory for hackathon participants, because we can accommodate only a limited number of people. Lectures will be open and if you only plan to watch them, you don’t need to participate.

How long will it be?

NGSprit will take place from 8th to 15th of September 2021. In the early afternoons (CET) of working days we will spend 1.5-2.5h introductory sessions, lectures and workshops. Later, every working day you will have at least 1h to discuss the tasks at hand with your mentors. The exact timing and form of meetings will be decided by your mentors and their teams. Beside lectures, workshops and sessions with mentors you will work with your team at your own pace. We don’t plan any activities on the weekend, but you are free to decide when you work on the tasks.

How will I communicate with my team and mentors?

The main communication platform will be NGSchool Discord where every team will have their own text and voice channels. You will use a voice channel to meet with your mentors every day. You can also write to your mentors at any time and they will answer you as soon as they can.

Is the presentation of results at the end of NGSprint obligatory?

Yes, every team will present their results to other participants. However, it will be neither an assessment nor a contest, but an opportunity to learn for everybody. We are convinced that by presenting and discussing our work, we get valuable experience and skill.

Can I join together with my own team?

If you would like to work with your colleagues, you all should register and select the same NGSprint topics. However, please remember that there is a participant selection process and registration does not guarantee a place.

Can I apply without having my own team?

Yes. Later you will form a team with people interested in similar topics.

Do I need any specific background to participate?

Depending on the topic. We do not have hard entry requirements, but we would suggest you try to familiarize yourself with the requirements listed in topic descriptions. For an introduction to many of these, check out our NGSeminars.

Organisers

• Szymon Grabia, Medical University of Lodz, Poland
• Urszula Smyczyńska, Medical University of Lodz, Poland
  
• Kasia Kędzierska, WCHG, OX, Oxford, GB
  
• Karolina Sienkiewicz, Weill Cornell Medicine, Cornell University, USA
  
• Anamaria Elek, CRG, Barcelona, Spain
  
• Samantha Filipów, CECAD, University of Cologne, Germany
• Gladys Wojciechowska, Medical University of Bialystok, Poland
• Natalia Zawrotna, University of Virginia, USA