MY_SKILLS

I studied Environmental Biology (specialising in aquatic ecology) and Computational Methods of Physics (learning how to model physical processes using computers). Since then I have worked in scientific research improving my skills with each project.

For more detailed info on projects I did, see the tab RESEARCH. To learn where I gained these skills, see the tab BIO.

THINGS I DID

Python : I coded various scrips combing through the directory tree in search of text files containing specific data (e.g. simulation results with particular parameters). The scripts segregate, compute, do statistics and plot the data • Simple webpage crawler that gathered data on RNA sequences from a database web page that was no longer maintained (abandonware) • A bunch of Python scripts for cluster computer that automatically set parameters, launch simulations (written in C++) and compare their results with empirical data. We only have to pick the cutest graphs after few days of computations☺ • A lot of text data parsers.

C++ : I wrote from scratch two agent-based simulations and extended one already existing . They were all designated for launching on cluster computers. This programs simulated life and evolution of the population of agents (bacteria, generic vertebrates, viral antigens) • Code mostly rely on STL objects (vectors, sets, etc.) and some of Boosts routines • I used OpenMP for palatalisation of computations (I aimed at course parallelisation).

Biology : I created a small database of non-coding RNA (before large repositories became available) • Designed and performed experiments with small animals (zooplankton, fish) • Had some experience with laboratory methods of molecular biology • Created and developed a number of agent-based simulations in evolutionary biology and epidemiology.

CODING & COMPUTER

Python Coding for data analysis and data visualisation: Numpy, Pandas, Scipy, Matplotlib, Seaborn, a bit of Peewee, analysis of voluminous data (that cannot fit in RAM in one chunk)
C++ Intermediate coder using C++ for building custom (and resonantly fast) simulation of complicated biological processes, big fan of the Standard Template Library and Open MP
Linux Power user: scripting in Bash and a bit in AWK, good understanding of the system’s backbone, no GUI required, using Linux since 2004
Version control Using git for version tracking and code sharing
HPC Running computations on remote high power cluster computers, automation of large volumes of computations that can run for days without supervision
MATLAB Some experience in the past, later switched to Python (Matlab’s license is a bit pricey)

 

MATHS & STATS

Basic math Three years of undergrad studies at a physics faculty: formal logic, calculus, probability theory, fuzzy set theory and things like that
Optimisation Fitting models, selecting parameters
Stats ANOVA and linear models, bootstrapping, solid foundation in understanding mathematics behind statistics
ML / AI Soon… learning it

 

SCIENCE & RESEARCH

Ecology Graduated in Environmental Biology doing experimental aquatic ecology at the Department of Hydrobiology, University of Warsaw, I worked on the ecophysiology of plankton and fish
Evolution I studied evolution of bacterial genomes, later non-coding RNA and later major histocompatibility complex (MHC) genes
Modelling biology Agent-based modelling is my research speciality since few years, I do custom simulations of problems too complex to use more traditional mathematics
Scientific writing Published author of research articles in English and Polish, completed number of courses dedicated to scientific writing, author of pop-science pieces in Polish

 

SOFT SKILLS

Languages English (very good), Polish (native), Russian (communicative), German (basic)
Teamwork Contributing member of a team up to 30 members • leading a small team up to 6 members • working in a multinational environment • working in groups scattered across institutions, towns and countries • using networking and data sharing software such as Slack, GitHub, BitBucket
Social media Responsible for social media presence of grassroots academic organisation Obywatele Nauki (2012-2018, Facebook, Twitter) and Nauka dla Przyrody (2017-present, Facebook, Twitter). I learned to write short notes containing condensed information