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a-kramer/README.md

📚 Education

1995-2002
Carl-von-Ossietzky-Gymnasium in Berlin (HC82+M3 Berlin, Germany). We could choose two main subjects for in-depth study, mine were Biology and Physics.
2002–2008
Studied Physics at Humboldt-Universität zu Berlin. The Science Campus is in Berlin-Adlershof (CGMH+4V Berlin, Germany). There I obtained my Diploma (grade: good).
2009-2016
Doctoral studies at the SimTech Graduate School, within the University of Stuttgart. I worked as a teaching assistent and did research in the area of systems biology within the Institute for Systems Theory and Automatic Control. I obtained the title of Doktor der Ingenieurwissenschaften (Dr.-Ing.), which is roughly equivalent to a PhD.
2016-2020
Postdoctoral researcher at KTH Royal Institute of Technology, school of Electrical Engineering and Computer Science (EECS), CST department. I continued to work on the topic of systems biology and simulations.
2020, current
I work as research specialist at Karolinska Institutet, in the Science for Life Laboratory, Solna (922F+59 Solna).

Details

These are some of the tasks, duties, and projects I was involved in:

2007–2009
During my studies at Humboldt University, I was a student-assistent at the Konrad Zuse Institute, Berlin. I worked in the department for high performance computing. My tasks included scripting, testing of software, and hardware setups. One example is a Gentoo GNU/Linux machine that converts incoming email to text messages (SMS) to inform staff of error mesages from the compute cluster (while not at their desks). This involved Perl and Bash scripting as well as procmail configuration.
2009–2014
After graduation from Humboldt University, I began work as doctoral student and teaching assistent (TA) at the Institute for Systems Theory and Automatic Control (IST). My responsibilities included:
  • TA for the course dynamics of biological systems (about nonlinear dynamics); TAs design exercise problems, exam problems, and lead the in-person exercise groups.
  • TA for the course statistical learning and stochastic control; making small statistics demonstrations in R
  • Administration of a small simulation machine (Gentoo, GNU Linux) for the systems biology group
  • I adminstered the group's library (scientific literature), ordering books, loaning books to students.
  • supervision of student theses; this is a manuscript that students write before a master's thesis or diploma thesis.
  • I built a webpage (using a template) for a colloquium at the institute: a registration mechanism, and the program of the event
2009–2015
As a doctoral candidate, I contributed to articles in proceedings of conferences, made posters, held presentations (as all PhD students do).
2012
In summer 2012 I was a visiting researcher at University College London (UCL, Statistics Department). There I began contributing to a c library dedicated to Markov chain Monte Carlo. I worked on this library and built an MCMC sampler with it. Lessons from working on this fueled our work on the UQSA r-package.
2019–2022
At KTH I continued to assist in teaching as a postdoc. I contributed to the course Applied Programming and Computer Science for physicists

💻 Programming Languages

The language I have enjoyed working with the most is C, with Makefiles as build system. No cmake, no autotools.

I am most proficient with:

  • C and Makefile (mostly GNU Make)
  • bash, any POSIX shell and all of the utilities asociated with shell scripting
  • R
  • GNU Octave (and by extension matlab)

Here are more details about programming languages: programming languages

Note

I strongly prefer Free Software over anything proprietary. I oppose software patents. I like frugality and minimalism in software.

💬 Human Languages

I speak these languages:

  • English (pretty well)
  • German (like a native)
  • Russian (with a german accent, and slowly), but I understand everything (probably).

By now I understand a bit of Swedish, but learning Swedish is is a huge TODO item for me.

These are Conferenes that I attended

Year Place Conference Contribution
2009 Liège CASYS short article
2010 Dortmund DAGStat presentation
2010 Amsterdam ICCS article in proceedings
2010 Yokohama MCS article in proceedings
2011 Göttingen SDMBM presentation
2012 Berlin MASAMB poster
2013 Dresden SDMBM poster
2017 STockholm Nordic Neuroscience (participation)
2017 Glasgow 5th Human Brain Project Summit (participation)
2019 Berlin INCOME2019 presentation
2021 virtual INCOME2021 poster

I have also taken part in many SeRC annual meetings, sometimes as a member, sometimes as one of the organizers.

📑 Publications

On orcid, you'll find a list of my publications.

Pinned Loading

  1. mcmc_clib mcmc_clib Public

    c program for simplified manifold MALA sampling of ODE model parameters

    C++ 8 1

  2. COVID19 COVID19 Public

    model of how the infection may be spreading

    MATLAB

  3. SBtabVFGEN SBtabVFGEN Public

    Convert a Model written in SBtab, saved as an Open Document Spreadsheet to a VFGEN vector field file

    R 3

  4. Systems-Biology-Scripts Systems-Biology-Scripts Public

    Scripts that are useful for the processing of parameter samples of dynamic models

    MATLAB

  5. rgsl rgsl Public

    R gsl solver interface

    C 1

  6. RPN-derivative RPN-derivative Public

    Calculates the derivative of anexpression given in reverse polish notation

    Shell 1