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Workshops and Courses offered through the EpiCrossBorders program are developped around the interests of our students. Students in the program are involved with the process of deciding what kind of courses we should develop. When a course is designed feedback from our students allows us to further update our courses to make sure our course offering develops with the needs of our students and our community.

Below you can find the courses and workshops that are currently active in the EpiCrossBorders program. This is in addition tot he courses and workshops offered in the overarching programs at the HMGU (HELENA) or the Edinburgh graduat programs. EpiCrossBorders operates within these programs.

TAC symposium

The role of the Thesis Advisory Committee (TAC) is to support you during your PhD. The members of your TAC are there to provide you with advice and recommendations for your thesis project and to help you to make your project a success. But how can you make sure you get the advice you need to make your project a success?

Critical reading and listening skills as well as providing critical supportive feedback are fundamental skills in science and life in general. How do you evaluate someone else’s work? By evaluating the works of others you will also gain an understanding on how others may evaluate your work.

In this course we will support you in the preparation for your first TAC meeting and start your training in the above mentioned skills. We will do this through a peer to peer approach where participants in the course provide feedback to each other's written proposals and the presentations of their proposal in a mini symposium.

You can then take the feedback from this course to further improve your TAC proposal and presentation for your actual first TAC meeting.

The emphasis of this course is on how you present your proposal (written and orally), feasibility, back up strategies, time table etc. Scientific details are to be discussed with the respective group leader and lab.

 

Lecture Journal Club Series

As stated on the main page of this website epigenetic processes form one of the key interfaces between cells and organisms and their direct environment. Epigenetic processes play important roles in embryonic and organism development, disease development, the response of organisms to stress (climate change and other stress factors) and much more.

The improvement of our understanding of epigenetic processes is key in facing some of our major challenges. 

This high diversity in the field of epigenetics is reflected in the composition of our epigenetics community and thus the projects for which we recruit our students. This in turn results in a broad range of expertises and backgrounds among our students.

The TAC symposium course aims to do two things:

1. Teach the core concepts of Epigenetics to all the students in the program and provide them with a solid Epigenetics Background

2. Allow the students to discuss and network with different group leaders in our community

In the Lecture Journal club you will discuss 11 key aspects of the field of Epigenetics with 11 different experts from our community. By learning through participation you will not only gain the required back ground, you will also train your discussion and listening skills. In addition to that you will continue with the formation of your network within the community.

GALAXY course

There are currently two courses that are taught with the Galaxy platform. These courses are developed and taught by the HMGU Bioinformatics core facility. Students within the EpiCrossBorders program can list one of these for the requirements of the program, but are free to participate in both. Both courses require basic R and Rmarkdown experience offered in courses fromt the HMGU Bioinformatics core facility.

Additional information on both courses and registration options can be found here

1: Differential gene expression analysis using RNA-Seq data and the Galaxy platform

This course covers topics regarding experimental design, introduction and considerations for NGS sequencing, hands on sessions to get from raw sequencing data to count matrices using the Galaxy[1] platform, QCs for RNA-Seq data, sample visualizations, statistical analyses using R and the DESeq2 package[2] and the creation of reports using RStudio and R Markdown[3]. You will create an integrated report using RStudio and R Markdown [3] and have the opportunity to analyze your own data or a published dataset of interest.

Topics

  • • Fundamentals of RNA-seq analysis
  • Processing of RNA-seq data using Galaxy
  • Visualization of sequencing data and analysis of RNA-Seq data
  • Integrated RNA-Seq data analysis with R and RStudio
  •  

2: Differential protein binding to DNA using ChIP-Seq data and the Galaxy platform

This course covers topics regarding experimental design of ChIP-Seq experiments, introduction and considerations for NGS sequencing, hands on sessions to get from raw sequencing data to peaks using the Galaxy platform [1], QCs, sample visualizations and the statistical analyses of differential protein binding to DNA using R and the DiffBind package [2]. You will create an integrated report using RStudio and R Markdown [3] and have the opportunity to analyze your own data or a published dataset of interest.

Topics:

  • Fundamentals of ChIP-seq analysis
  • Processing of ChIP-seq data using Galaxy
  • Visualization of sequencing data and analysis of ChIP-Seq data with DiffBind Integrated
  • ChIP-Seq data analysis with R and RStudio 

Protein purification

Recombinant proteins are essential tools in biomedical science with a multitude of applications in basic as well as clinical science. Generating a recombinant protein requires the use of an expression system. Selection of an appropriate expression system is dependent on the characteristics and intended application of the recombinant protein and is essential to produce sufficient quantities of the protein. In this course, we will take advantage of Escherichia coli as an expression system to overproduce a soluble 6xHis-tagged form of the tobacco etch virus (TEV) protease and purify it to homogeneity using an Äkta Pure 25 FPLC chromatography system. The purification protocol consists of a Talon affinity purification and subsequent ion exchange chromatography. TEV protease is a commonly used reagent for removing affinity tags from recombinant proteins by site-specific endoproteolysis. Thus, the activity of the purified protein will be tested in a biochemical cleavage assay. This course will give the students all necessary theoretical background as well as hands-on training on an Äkta-FPLC system to master future recombinant protein production projects.

This course is developed for the EpiCrossBorders program by Dr. Stephan Hamperl (IES)

 

This course has been on hold due to the Covid-19 pandemic, when the situation allows this course will become active

Scientific graphical design

A key aspect of scientific publication is understanding how to clearly and accurately represent your data. Each figure should convey one key message without misleading the reader. Therefore each aspect of a figure must be optimised to effectively communicate that message. For successful implementation, understanding and acknowledging key design elements of figures are crucial. Here we discuss the contribution of several elements:

- cognitive science for perception and color
- image rendering
- data depiction and design.

This course will dive into these topics focusing on figures for manuscripts and scientific publications:

Principles of design and graphic communication:

-Theory of data visualization
-Ethics of data representation
-Elements of graphic design
-Principles of vector editing and compositing in Inkscape
-Harmonisation and context in manuscript preparations 
-Journal submissions

This course is developed for the EpiCrossBorders program by Dr. Celia Martinez-Jimenez (HPC) and Dr. Rhîannan Williams (ING).

This course is an adaptation from the original course “Scientific Figure Design” by Simon Andrews, Anne Segonds-Pichon and Boo Virk (Brabraham Institute).

 

Image Computing

Many scientific projects require the analysis of large numbers of images. At some point, it becomes more efficient to develop automated methods instead of performing analyses in a manual way. This also enhances the standardization and reproducibility of your analysis methods.

In this course, we will discuss the basics of image analysis, feature based methods and deep learning based approaches. We will also have hands-on sessions and try out a couple of potent tools available to us like FIJI and cell profiler. For students with a programming background, we will look into the customization of algorithms with Google Colab.

 

This course was developed for the EpiCrossBorders program by Dr. Carsten Marr, Ali Boushehri and Valerio Lupperger from the ICB

Scientific writing

Publication writing, an art in itself, how does one deliver the right message? Where to start? What makes a good publication? All daunting questions, especially when one writes their first publication. To achieve the optimal support to our students, we aim to offer such a course at the time where a student is ready to start writing his or her (first) publication. As all doctoral (PhD) projects move at their own pace, different students are ready to write at different times in their time as a doctoral student. Because of this we have opted to work together with Iain Patten who provides open courses that allow students to participate when they are ready.