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.

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.

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.

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 

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.