Welcome to the blog on scientific computing at the Max-Planck Institute for Evolutionary Biology

In this blog, we summarize the activities in the Scientific Computing Unit. In particular, we cover topics such as

* Tips and Tricks, Dos and Don'ts in scientific computing
* Outlines and summaries of ongoing research and software projects
* Updates and new releases from our software repositories
* Recommended readings, videos, websites

Importing data to OMERO

 Posted on October 25, 2021  |  

Getting your data into the database is one of the most frequent tasks when working with OMERO. There are two different ways to import data into OMERO: Via the desktop app OMERO.insight or via the commandline client that comes with OMERO.py. Both software packages can be found on the OMERO download site https://www.openmicroscopy.org/omero/downloads/. While the desktop app is easy and intuitive to use, a drawback of using it is that it must remain open while the data is uploaded. [Read More]
omero,  images,  data  management,  command  line,  insight 

Programming Courses at MPI Evolutionary Biology

 Posted on October 2, 2021  |  Carsten Fortmann-Grote

As every year, some PostDocs and Staff Scientists offer courses on computing, programming, data analysis and visualization and related topics. Requirements: Some courses require that participants already have certain levels of experience and knowledge. Before signing up, please assess for yourself if you feel comfortable with these requirements. If in doubt, please contact the course responsible. During the course, there will not be enough time to bring everybody up to the expected level before starting the course program. [Read More]
courses  workshops  teaching  programming  software development  git  python  R  unix  command line  bash  terminal  SLURM  HPC 

Jupyter lab tutorial

 Posted on May 6, 2021  |  Carsten

On May 5 & 6 2021, I took part in the Workshop “Kompetenz Forschungsdatenmanagement” organized by the Max Planck Digital Library. Day 2 featured a full session on “Reproducible Science with Jupyter” with a presentation by Hans Fangohr (slides available here) followed by an interactive hands-on tutorial. In part 1 of the tutorial, I step through a data analysis workflow based on the Johns-Hopkins University CoViD19 dataset from github. Part 2 and 3 are about Bayesian Inference of SIR model parameters, kindly provided by Johannes Zierenberg from MPI Dynamics and Selforganization. [Read More]
jupyter  notebook  reproducible science  fair  covid  pandas  visualization 

Dask and Jupyter

 Posted on January 22, 2021  |  Carsten

Parallel python with dask and jupyter The dask framework provides an incredibly useful environment for parallel execution of python code in interactive settings (e.g. jupyter) or batch mode. Its key features are (from what I’ve seen so far): Representation of threading, multiprocessing, and distributed computing with one unified API and CLI. Abstraction of HPC schedulers (PBS, Moab, SLURM, …) Data structures for distributed computing with pandas and numpy syntax Dask-jobqueue The package dask_jobqueue seems to me to be the most userfriendly if it comes to parallelization on HPC clusters with a scheduling system such as SLURM. [Read More]
parallel  multiprocessing  python  dask  jupyter  scheduler  slurm  mpi 

Research Software Development Workshop 2020

 Posted on December 14, 2020  |  Carsten

On Dec. 10 & 11, Nikoletta Glynatsi and I ran our first Workshop on “Research Software Development”. Far from appraising myself, but judging from the feedback, it was a big success. For two days, we taught best practises in writing software (exemplified with python), using git for version control, collaborating on gitlab projects and employing gitlab’s built-in continuous integration tools to run automated tests and build a reference manual. All material from the workshop, including all presentations and code examples are available under terms of the MIT License from this gitlab repository: https://gitlab. [Read More]
git  python  coding  software tests  CI  gitlab 

Running matlab code on HPC with SLURM

 Posted on December 14, 2020  |  Carsten

Running MATLAB scripts on HPC Today, the question came up how to run MATLAB code on HPC featuring a SLURM scheduler. The syntax for running matlab on the command line is indeed a bit counterintuitive, at least if you are (like me) used to running python or R scripts. Example SLURM script The following snippet is an example for how to submit a matlab script for execution on an HPC Server with the SLURM scheduler: [Read More]
scheduler  command line  syntax  script  job submission 

Converting jupyter notebooks with embedded images to pdf.

 Posted on December 9, 2020  |  Carsten

Inserting images in a jupyter notebook is just drag and drop: This will automagically produce the image link at the drop position. And after executing the cell, the image is rendered So far so good. But ever tried to convert a notebook with embedded images to pdf or html (slides)? My first guess was: Menu -> File -> Export Notebook As -> PDF. However, this immediately runs into Error 500 tracing back to latex not being able to locate the image attachment:5444. [Read More]
attachment  images  nbconvert  pandoc 

Rent-a-Scientist 2020

 Posted on November 27, 2020  |  Carsten

I just finished my lecture at Heinrich-Heine-Schule Büdelsdorf on “Evolution und Künstliche Intelligenz.” (“Evolution and Artificial Intelligence”). Slides are here.