Oslo Bioinformatics Workshop Week 2022

microRNA profiling and sequence analysis

Date: Monday 12 December 2022 9:00-12:00 13:00-16:00 Add to calendar

Description

This workshop will teach the basics of NGS microRNA analysis from raw data processing (and retrieval from SRA), to microRNA profiling & DE-analysis and creation of publication-grade plots (R).

We will also present the Galaxy-based tool MirMiner for de novo prediction of microRNAs.

Target audience

PhD students and above

An introduction to Snakemake and Snakemake workflows

Date: Friday 09 December 2022 9:00-12:00 Add to calendar

Description

In this workshop, I am planning to give a short introduction to the Snakemake workflow management system. This entails installation, running the simple scripts via Snakemake, using some advanced features of Snakemake, and how users can use Snakemake in their daily tasks.

Target audience

Master students and PhD students who wants to create bioinformatics pipelines

Genome assembly, curation and validation

Date: Tuesday 13 December 2022 9:00-12:00 13:00-16:00 Add to calendar

Description

The advent of such projects as Earth Biogenome Project (EBP) and European Reference Genome Atlas (ERGA), and our own Earth Biogenome Project Norway (EBP-Nor) is partly due to the fact that creating high-quality chromosome-level genome assemblies for almost any species is currently possible. However, sequencing technologies are still not at the point where chromosomes are reconstructed from end-to-end without gaps, so the use of Hi-C to scaffold contigs made from long reads is essential. Validation and statistics are important parts of the assembly process. For instance, the input reads can be used to assess the heterozygosity of the sample, in addition to giving genome size and ploidy estimations. In different stages of the assembly process, investigating the presence of expected genes and comparisons of kmer profiles of the assembly to the reads, can be used to assess the quality of the assembly. In addition to the target species, contaminants/symbionts/cobionts can sometimes occur, and sequences from these need to be identified and separated. After scaffolding and removing possible contaminants, the genome assembly needs to be manually curated, a process that can fix assembly errors and improve the assembly overall. In this workshop we will touch upon these matters and discuss the tools often used to do these analyses.

Target audience

Anyone interested in learning more about genome assemblies and how to make them

High-performance computing in bioinformatics with Numpy/bioNumpy

Date: Wednesday 07 December 2022 9:00-12:00 13:00-16:00 Add to calendar

Description

Python is becoming an increasingly popular choice for computational biology and bioinformatics analysis, as it is easy to learn, is flexible and enables rapid data analysis and tool development. However, methods and workflows implemented in Python often don’t scale computationally to large data sets. In this workshop, we show through lectures, live-coding and exercises how the Python packages NumPy and BioNumPy can be used to write efficient Python programs that can handle big datasets and problems that we currently encounter as bioinformaticians. The first part of the workshop will cover the basics of Numpy and BioNumpy, while the second part is devoted to working on real world biological applications using data from sources such as fastq, fasta, bed, vcf, bdg, gtf, bam and sam files.

Target audience

All stages, fields and interests.

Bioinformatics beginner's course - an introduction to whole genome sequencing

Date: Wednesday 07 December 2022 9:00-12:00 Add to calendar

Description

After giving a short overview of Next Generation Sequencing, paired-end reads and the difficulties of whole genome assembly, we will address quality control of the raw data (FastQC), common file types and adapter/quality trimming. Differences between de novo assembly and mapping to an annotated reference genome will be explained, and we will present different software solutions and tools.

Target audience

Students, PhD student, Postdocs, Medical doctors, hospital employees

Responsible development in Machine learning

Date: Thursday 08 December 2022 9:00-12:00 Add to calendar

Description

Have you ever heard the phrase “If you can’t reproduce your results, you can’t trust them”? Bioinformatics software, as any software product, is vulnerable to feature major bugs that invalidate scientific findings and great tools can be unused if others fail to run them on their computers. The good news is that software engineering solutions have developed over the years so that we can implement good practices without in-depth knowledge in computer science. This is one of the two focus points of this workshop. The second focus is machine learning (ML). There is an increased interest towards machine learning within the bioinformatics society, driven by spectacular results. Trust can be especially important with ML software, as the models will always predict something in which a keen eye may find something interesting, even if the initial code has a major bug and the predictions are nonsense. As most popular ML software has been implemented by others, it is common to import large software ecosystems with a fair amount of dependencies. During this workshop we will code a small ML project to predict disease outcomes from publicly available patient data. While working on this mini project, we will give special emphasis on dependency management and software quality with focus on reproducibility, maintainability, readability, and extensibility of your code.

Target audience

People who are interested in improving their coding is welcome. We hope to have a nice discussion involving the insights of senior professionals as well as early career scientists.

Create a data management plan with DSW

Date: Monday 12 December 2022 9:00-12:00 Add to calendar

Description

This workshop aims at providing a hands-on session on creating a data management plan (DMP) using the Data Stewardship Wizard (DSW), a dynamic web forms system provided by ELIXIR Europe. The Norwegian node of ELIXIR is curating a national instance of DSW (https://elixir-no.ds-wizard.org) and provides a DMP form customised for life scientists in Norway. In this workshop, the primary instructor will initially walk the audience through the features of DSW while explaining the information to be captured in a DMP. As part of this demonstration, the instructor will show how to create a DMP, starting either from scratch or from a set of recommendations based on specific scientific domains including, among others, sequencing, light microscopy and high-throughput screening. A demonstration of how to work collaboratively on DMPs and how to export them to a document compliant with national and international funding bodies' requirements will also be given. In the second part of the workshop, the participants will work, individually or as groups, on a DMP for projects they are involved or for projects of interest. The two instructors will give advice and bring up interesting discussion points based on feedback from the participants. Depending on the audience, a discussion on how to modify a questionnaire or on other, more technical aspects might occur as part of the workshop.

Target audience

This workshop targets researchers at any career stage with responsibility for a certain project or the data generated within a project. Data specialists or technical personnel in the life sciences that want to learn more about DSW are also welcome.

Workflows for multi-omic data for genome regulatory annotation

Date: Thursday 08 December 2022 13:00-16:00 Add to calendar

Description

This workshop will demonstrate workflows for turning raw sequence data from RNA-Seq, ATAC-Seq, and ChIP-Seq assays into descriptive results, and how to combine these multi-omic results into annotations of chromatin states and regulatory regions in the genome.

Target audience

Researches who wish to use workflows for processing their sequencing data from ATAC-Seq, ChIP-seq, or RNA-Seq assays to results. Researchers interested in annotating genome chromatin state, or regulatory regions.

Multi-omics data integration analysis

Date: Friday 09 December 2022 13:00-16:00 Add to calendar

Description

In this workshop I will discuss challenges of working with high-dimensional biological data and introduce a machine-learning view of multi-omics data integration analysis. In particular, I will focus on what is conceptually meant by data integration and how it should be evaluated. Further, I will give an overview of a few main analytical techniques for multi-omics pre-processing (feature selection) and integration such as graph-based, matrix factorization and Bayesian methods. Finally, I will demonstrate a few practical examples for supervised and unsupervised integration of single cell multi-omics data.

Target audience

Master students, PhD students, postdocs, PIs

Microscopy Image Processing with Image J

Date: Monday 12 December 2022 9:00-12:00 13:00-16:00 Add to calendar

Description

Optical Image Processing with ImageJ.

Target audience

Master students, phd student and postdocs

Species occurrence data publication to GBIF

Date: Wednesday 07 December 2022 9:00-12:00 Add to calendar

Description

This workshop aims to publish species occurrences using the Integrated Publishing Toolkit (IPT) to GBIF. Biodiversity data published in this way follow Open data and FAIR data principles. We'll be using the Darwin Core data standard and get an overview of its structure. Participants are encouraged to bring their own data for publishing.

Target audience

Anyone generating or using biodiversity data based on species (taxons or species concepts)

Introduction to gene expression regulation by transcription factors and its computational analysis

Date: Tuesday 13 December 2022 9:00-12:00 Add to calendar

Description

Gene regulation by transcription factors (TFs) is a key process in cells, controlling when and where sets of particular genes will be transcribed. This precise control is important for cell growth and differentiation, but it also means that perturbation in such mechanisms can lead to diseases, e.g. cancer. Various experimental techniques were developed to map transcription factor binding locations along the genome. The most used nowadays is ChIP-seq. Resulting experimental data requires dedicated computational tools for data analysis and interpretation. A bouquet of such tools is already available, varying from peak callers and motif discovery tools to more complex deep learning algorithms. In this workshop we will introduce the transcription factors and how they are controlling gene expression. We will describe the properties of transcription factor binding, such as sequence binding motifs. Furthermore, we will discuss available in vivo and in vitro experimental techniques that help capture transcription regulation events. Finally, we will walk through the data analysis produced by different techniques. This will focus on TF motif discovery and enrichment, TF binding site determination. We will show a few freely available resources that store TF binding profiles and sites and demonstrate a selection of online tools for data analysis. The last part of the workshop will consist of Q&A (participants can bring their project-related questions) and a hands-on exercise.

Target audience

Any career stage

Introgression detection

Date: Wednesday 07 December 2022 13:00-16:00 Add to calendar

Description

Genome sequencing has revealed that many species have exchanged DNA with other species due to past hybridization – a process called "introgression". A number of methods have been developed to detect such past hybridization and introgression. Among these is the "ABBA-BABA test" and its test statistic, the D-statistic, which was first applied to a comparison of human and neanderthal genomes, and has since supported introgression in a large number of organisms. A fast implementation of this test and related statistics is the one in the program Dsuite, which will be taught in this workshop.

Target audience

Evolutionary biologists of any career stage

A hands-on introduction to NeLS and usegalaxy.no

Date: Thursday 08 December 2022 13:00-16:00 Add to calendar

Description

This workshop covers an introduction to the Norwegian e-Infrastructure for Life Sciences (NeLS) and usegalaxy.no. These services, both administrated by ELIXIR Norway, provide national users with data storage and the possibility to run analyses and define workflows in a reproducible way. The workshop will cover a general introduction to NeLS and its 3-layer tiered storage system with a specific focus on data transfer. A general introduction to transferring files between NeLS and usegalaxy will also be provided, followed by a dedicated session about the standard galaxy tools and "histories" for reproducible analysis. The final session will cover how to create and run workflows on usegalaxy and how to share them with other users. Each session will start with a short presentation, followed by a detailed hands-on session.

Target audience

Researchers in life science/bioinformatics

Statistical principles in machine learning for small biomedical data

Date: Tuesday 13 December 2022 9:00-12:00 Add to calendar

Description

A central problem in machine learning is how to make an algorithm perform well not just on the training data, but also on new inputs. Many strategies in machine learning are explicitly designed to reduce this test error, possibly at the expense of increased training error. These strategies are collectively known as regularisation and they are instrumental for good performance of any kind of prediction or classification model, especially in the context of small data (many features, few samples). We will discuss basic connected concepts of generalisation, overfitting, bias-variance trade-off and regularisation and will illustrate the principles with penalised (generalised) linear regression models, with ridge, lasso and elastic net penalties as prominent examples. Finally, we will present the idea of structured penalties and priors, which can be tailored to account for structures present in the data, e.g. multi-modality or complex correlation structures. We will use examples from large-scale cancer pharmacogenomic screens, where penalised regression and alternative Bayesian approaches are used for predicting drug sensitivity and synergy based on the genomic characterisation of tumour samples. In the hands-on tutorial we will use R to perform an integrated analysis of multi-omics data with penalised regression.

Target audience

Graduate, post-graduate students and researchers at any level who are interested in applying machine learning methods to small data (few examples but potentially many features) or noisy data (e.g. biomedical data).

Container technologies and their use in GWAS analysis

Date: Friday 09 December 2022 9:00-12:00 Add to calendar

Description

In this workshop, we will start with basic concepts of container technologies like Docker and Singularity followed by instructions on how to use them. Then, we will briefly touch on the basics of Genome-wide Association Studies (GWAS) and then we will examine how and why we can use containers in GWAS analysis.

Target audience

Any level who is willing to learn how to perform GWAS analysis using containers.

Introduction to Git and Development Cycle

Date: Monday 12 December 2022 13:00-16:00 Add to calendar

Description

During software development when collaborating with other developers, it is essential to perform version control to ensure the codebase is maintained properly. This workshop aims at introduce Git in the practical development cycle.

Target audience

Anyone who would like to develop software.

Clustering and plotting of single-cell expression data

Date: Thursday 08 December 2022 9:00-12:00 13:00-16:00 Add to calendar

Description

In this workshop we will explore the clustering and plotting of single-cell data based on gene expression. We will start with a theoretical introduction to the stages upstream of generating a Seurat object looking into model systems vs non-model systems, QC, cut-offs etc. Following is a hands-on RStudio session exploring the Seurat object focusing on data filtering, cell clustering based on gene expression, cell cycle regression, cluster annotation and data integration. Please note that this course will NOT cover analysis of multi-modal/multi-omics single-cell data.

Target audience

This workshop is for anybody interested in single-cell expression analysis, regardless of career stage, who is relatively comfortable with using R as a tool. The level will be introductory with respect to analysis, but discussion around the various strategies demonstrated is encouraged as single-cell analysis follows no "standard recipe". You are welcome to discuss your own data/single-cell plans at the end of the workshop.

Hands-on introduction to uniFAIR: a systematic and scalable approach to research data wrangling in Python

Date: Friday 09 December 2022 13:00-16:00 Add to calendar

Description

Life science researchers often need to extract, manipulate and integrate data and/or metadata from different sources, such as repositories, databases or flat files. Much research time is spent on trivial and not-so-trivial details of data wrangling: to reformat data structures; clean up errors; remove duplicate data; or map and integrate dataset fields. Software for data wrangling and analysis, such as Pandas, R or Frictionless, is useful, but researchers still regularly end up with hard-to-reuse scripts, often with manual steps. uniFAIR is a new Python library with a systematic and scalable approach to research data wrangling. With uniFAIR, researchers can import (meta)data in almost any shape or form: nested JSON; tabular (relational) data; binary streams; or other data structures. Through a step-by-step process, data is continuously parsed and reshaped according to a series of data model transformations. uniFAIR provides a catalog of generic task and subflow templates that the researcher can refine and apply to carry out the transformations needed to wrangle data into required shape. For large datasets, uniFAIR allows local test jobs on sample-sized data to be seamlessly scaled up to the full datasets and offloaded to external compute resources. Persistent access to the state of the data is available at every step. This workshop will introduce you to the technical and conceptual background needed to make use of uniFAIR, including the new type hints in Python. Participants will follow hands-on tutorials that are based on a series of use cases from genomics, proteomics, and machine learning.

Target audience

PhDs, Postdocs, Technical personnel. Interest and experience with programming in an academic setting. Several of the use cases will assume bioinformatics experience, so a background in bioinformatics will help. Most of the databases and ontologies in the use cases are from the biological domain. However, Python programming experience is more important than a background in bioinformatics.

Metagenomes meta-analysis: bioinformatic ecosystem from idea to data

Date: Wednesday 07 December 2022 13:00-16:00 Add to calendar

Description

In recent years, various large-scale research projects delivered increasing-well standardised metagenomic sequencing data to the public domain. Often times, such data is generated for pioneering or to address broad research questions, offering rich untapped information for meta-analyses and in-depth studies addressing more specific questions. First, we will explore such project's and realise that many data features can be exploited. Smaller projects also yield data that can be combined for insightful meta-analyses, which consist of collecting samples from independent sources and process them altogether to address new question, usually to test reproducibility or empower statistics with large sample sizes. For example, one might want to understand universal mechanisms by integrating soil with ocean samples from a given range of pH range, or to assess where genome lineages from a mass of air branch in a phylogeny containing genomes from underlying surface oceans. For this to be possible, meta-analyses both rely on and serve the quintessential purpose of standardization and the FAIR principles. It is important to interrogate metadata information to identify relevant samples before collecting all the sequence data files of a study. Thus, we will learn how to query public data repositories using different entry points (online and programmatically) and insist on metadata quality and content using python and visualization tools to measure potential for useful meta-analysis. The rest is simple engineering: we will use the NCBI SRA-Toolkit to download and format raw sequence data for bioinformatic processing and briefly discuss the technical challenges and avenues for metagenomics.

Target audience

This workshop is not intended for experienced computational scientists but rather for Master and PhD level biologists as well as senior biologists with little experience with R/python, willing to learn about accessing and collecting public metagenomic data.