This pipeline will overlay enhancer information from genomic regions supplied as BED files with RNASeq data to identify correlations between gene and enhancer expression. Pipeline can combine data from several types of experiments such as ATACSeq, GROSeq, CHIPSeq of various histone marks as well as removing ones that fall within coding regions. Requires both polyA depleted and polyA enriched sequencing from a similar set of samples. Created for project where we wanted to identify gene-enhancer pairs that change in skeletal muscle after intense exercise.

• Date: 2021
• Category: Workflow Automation

This Snakemake pipeline will analyze RNAseq data starting from fastq files to producing interactive visual reports for differential gene expression. Several of the most common aligners, read counters and packages for differential expression are included as well as the utility to specify SRA accession numbers and the pipeline will download the corresponding files. I always wanted to have a solution in which I can mix and match different aligners, counters etc. as well as easy way to handle custom parameters to different programs, so the pipeline is designed in a way that you can swap them in and out. Some of the most common workflows are predifined, but you can supply your own. This is a long running project that I started when I took over the bioinformatician duties in the laboratory and work started to pile up and I needed a easy-to-use scalable solution. It’s also a work in progress, I try to keep up with the developments in the field and add them as time permits. For code see my Github, previous simple solution with python and bash-scripts is for posteriority archived here

• Date: 2018
• Category: Workflow Automation

This is an automated workflow solution for an amazing package clusterprofiler that offers an easy way to run batch pathway analysis of an RNASeq dataset over a parameter space of your choice. It also produces interactive HTML reports with network graphs. This project was started when my colleagues and collaborators kept asking to re-run pathway analysis for their RNASeq data while slighly varying the analysis parameters and gene set selection. I also was not happy with the default network graphs that are part of clusterprofiler. They tend to get quite messy with larger gene sets, so I opted for interactive HTML reporting that allows for zooming and panning. You can find the source code in my Github. There are two additional tools that I developed for batch pathway analysis. First one is a interactive HTML report generator for Ingenuity Pathway Analysis from Qiagen that can be found here and a tool for running batch GSEA analysis with their commandline tools that can be found here.

• Date: January 2020
• Category: Workflow Automation

This project started when the requests started to increase for publication-ready graphs for the RNASeq analysis that I did as a part of my bioinformatician duties. Currently the project is mostly a collection of functions that produce the most common graphs such as PCA, volcano plots, annotated heatmaps and pathway analysis graphs with interfaces accepting data from the most common R packages for RNASeq analysis. I tried to keep the functions as flexible as possible, with hopes of turning it one day into an R package if the time permits.

• Date: January 2022
• Category: R Scripts

I have started this project to help a colleague to analyze time-series data for free wheel running protocol for mice experiments and then extended it to monitoring of metabolic cages as well. You can find the shinyapps of legacy projects here and here. In the meantime a nice app calR was released that can process the metabolic cage data, but lacks some of the functionalites that I would like, such as parameter correlation or binning of different frequencies, so I continue to develop my own solution. The original software connected to the mice running wheels had several issues, including bugs in time measurement/conversion and tendency to shut down from time to time so I developed a python project that is able to deal with irregular time series and interpolate missing measurements so it can be properly visualized. Also new equipments were bought in the meantime, so it’s nice to have a program that can unify the output formats from different sources. You can find the conversion scripts and visualisation framework in my Github.

• Date: 2017
• Category: Data Visualisation

I have developed this script and webpage as an easy to use interface to quantitatively analyze phosphorylation status of a particular protein from mass spectrometry data. Originally, we were trying to map a phosphorylation fingerprint of specific kinases on protein Dishevelled. At that time no commercial solution was available so we came up with our own workflow and then created a simple webpage interface so everyone in our group can use it for their own projects. It has served us well and we managed to publish several articles where we used it, nowadays there are commercial solutions available that probably have more robust calculations. You can find the source code in my Github and a working hosted version in my homepage.

• Date: 2014
• Category: Webpage

This a webpage for the Molecualar and Cellular Exercise Physiology group at Karolinska Institutet led by Prof. Jorge L. Ruas. We have decided that an externally hosted website should be created that would allow us to have indepth descriptions of our members and projects we are working on, together with a bit more attractive design. Originally, I used this opportunity to learn python MVC framework Flask in which it was originally created. Sfter realising we would need a VPS to run it, which was not really in the budget, I re-coded it in Laravel. It was a fun project, both coming up with design and displaying the information about our laboratory in an interlinked manner. You can find the Laravel source code in my Github and live version at ruaslab.science.

• Date: 2021
• Category: Webpage

During my Ph.D. studies at Masaryk University in Brno a scientific exchange program with Karolinska Institutet was created for Ph.D. students to improve mobility and gain expertise in new techniques. As a part of the endavor I was asked to create a webpage that would keep both students and funding agencies up to date with the ongoing events and developments in the program. Source code is available in my [Github] and live version in my homepage.

• Date: 2012
• Category: Webpage

After the relative success of the KI-MU program, I was contacted by Department of Physiology and Pharmacology, Karolinska Institutet to create a webpage and design materials for their upcoming conference about Macrophages and Microglia. The design materials included posters, flyers, nametags and abstract book. Webpage included authenticated section with forms to submit abstract information and author lists which then generated abstract book. The design is not exactly top-notch, at that time I was learning gradient meshes in Adobe Illustrator, so I think that reflected on it. At that time I was not aware of PHP frameworks so I coded everything from scratch. It probably was not the most beautiful solution, but it somehow worked. Nowadays I am glad for the availability of frameworks with all sorts of authentication modules and solutions. Source code can be found in my Github and live version in my homepage.

• Date: January 2012
• Category: Webpage

When writing my Ph.D. dissertation thesis, I decided to try my hand at creating all the illustrations and typography and cover myself. It started a long and a bit arduous journey to learn Adobe Indesign and improving my skills in Adobe Illustrator. Overall, even after many years I’m very satisfied with how it all turned out. For those who are interested, the whole thesis including illustrations is available in the Masaryk University thesis archive. At that time I was an avid reader of Order of the Stick comics, so I created illustration for my Ph.D. defence presentation in this style.

• Date: 2014
• Category: Illustration

Inspired by the figure design for my own disseratation thesis, I tried to help when my friends needed. This is a cover and a small set of illustrations for doctoral thesis about novel fuctions of Frizzled and Dishevelled. For some reason i like illustration style with sharp corners, which I tried here. The cover can be found here and the thesis is publicly available at Karolinska Institutet Open Archive.

• Date: 2018
• Category: Illustration

Soon after joining the laboratory of Prof. Jorge Ruas, I was kindly asked if I would help with a summary figure for a literature review in progress. It was a perfect opportunity to learn something new about the metabolism field that I had just joined, collaborate with my new colleagues, as well as develop my illustration skills. In the following years the figure was used and re-used as introductory slide in conference presentations and lectures both by our group and other researchers and it still makes me very proud whenever I see it ‘in the wild’. You can find the figure in a review Intercellular: local and systemic actions of skeletal muscle PGC-1s.

• Date: January 2017
• Category: Illustration

I have created a series of illustrations for a scientific review Kynurenines: Tryptophan’s metabolites in exercise, inflammation, and mental health that I also authored. It was fun and challenging project since I had to convey a lot of information in a very small space, while simultaneously keeping the visuals concise and self-explanatory.

• Date: January 2017
• Category: Illustration