Open Science Ambassodors Meeting 2024

 Posted on November 8, 2024  |  

I was at the 2024 Open Science Ambassodors Meeting in Berlin and gave a presentation on reproducibility in scientific and high performance computing. The presentation slides are at https://mpievolbio-scicomp.pages.gwdg.de/presentations/osa2024.pdf, the permalink is https://dx.doi.org/10.5281/zenodo.14051129. I also advertised our FAQ collection on good scientific practice in research software engineering, now online at https://mpg-rse.pages.gwdg.de/gwp-rse. At the workshop, we collected many more questions and also some answers. Thanks to the participants for your contributions! [Read More]
High  performance  computing,  reproducibility,  research  software  engineering,  good  scientific  practice 

Turning a pdf collection into jquery Datatable

 Posted on May 27, 2024  |  

Introduction As researchers, we give presentations. Over the last years, I gave somewhere between 2 and 10 presentations a year. What I need is a html document that lists all my presentations, their title, date of presentation and a link to the pdf document in a table. This table can then be included on my institutional home page. As a plus, I want the table to be searchable and each column to be sortable. [Read More]
RDF,  SPARQL,  metadata,  publications,  presentations,  knowledge  graph 

Numba and (vs.) SLURM

 Posted on October 18, 2023  |  

Introduction The python library numba provides (among others) just-in-time (jit) compilation for python. Python code can gain tremendous speed-ups without the need to rewrite a single line of code. Simply adding a decorator to a function such as illustrated in this example: import numba @njit def accelerate_me(): ... can lead to run times comparable to C or Fortran code. Let's make a concrete example, where we add random numbers in a for loop (not advised, but used here to demonstrate numba). [Read More]
SLURM,  HPC,  numba,  python,  scaling,  performance 

SLURM Array experiments

 Posted on October 18, 2023  |  

Background The SLURM array directive provides a simple and intuitive syntax to submit a job with multiple similar tasks to the underlying HPC system. To fully exploit this capability, a few things should be kept in mind. In the following, we will, starting from a simple, serial job, explore how the total run time of our job behaves when the `array` option is applied. job_001: A job with one task running on a single node on a single CPU This is likely the most simple job thinkable: We run the command `hostname` and let the process idle for 5 seconds. [Read More]
SLURM,  array,  mem-per-cpu 

Experimenting with the tripalv3 JSON+LD API

 Posted on December 30, 2022  |  

Experimenting with the tripalv3 JSON+LD API Introduction In this post I'm experimenting with querying the JSON-LD (LD stands for Linked Data) API of my Tripal3 genome database for Pseudomonas fluorescens SBW25. A little bit of background: Tripal is a content management system (CMS) for genomic data, based on the Drupal CMS framework. It facilitates setting up customized genomic database webservers to publish genome assemblies, annotation tracks, experimental and modeling data for one or several organisms. [Read More]
SPARQL,  Linked  Data,  RDF,  Pseudomonas  fluorescens  SBW25,  Knowledge  Graph,  triplestore,  genome  database 

Conversion of multiple sequence alignment file formats

 Posted on December 23, 2022  |  

Working on a multiple sequence alignment project, I wanted to calculate a distance matrix from a MSA dataset generated by progressiveMauve. The MSA file is in xmfa format. I could not find a tool that calculates a distance matrix directly from the xmfa file, so I searched for conversion utilities to other MSA formats, such as phylip, maf, or msa. This biostars forum entry always came out at top but the links provided there are dead. [Read More]
python  progressiveMauve  Mauve  phylip  xmfa  file format 

Querying metadata from omero in python

 Posted on December 23, 2022  |  Carsten

A colleague needed a table listing image ID, image filename, and number or ROIs for all images in a project. Here’s the python script I came up with: Query Metadata from omero Imports import omero from omero.gateway import BlitzGateway import pandas as pd import getpass Connect to omero conn = BlitzGateway('XXXXX', getpass.getpass(), host='omero.server.org') conn.connect() ········ True Retrieve datasets This sets up an iterator over the needed datasets but does not load any data into memory (yet). [Read More]
omero  metadata  python 

Example queries against the Pseudomonas fluorescens SBW25 knowledge graph.

 Posted on March 31, 2022  |  Carsten

Introduction In this post I will present example SPARQL queries against the Pseudomonas fluorescens SBW25 knowledge graph (SBW25KG). The knowlegde graph was derived from the manually created annotation in gff3 format, as explained in a previous post. The queries are run against a local instance of the apache-jena-fuseki triplestore. First, I set the endpoint URL and the maximum number of returned records: %endpoint http://micropop046:3030/plu/ %show 50 Endpoint set to: http://micropop046:3030/plu/Result maximum size: 50 Retrieve 10 CDS’s from the SBW25KG. [Read More]
SPARQL  RDF  Linked Data  Semantic Web  Knowledge Graph  queries  UniProt  Pseudomonas fluorescens  SBW25 

Turning a genome annotation into a RDF knowledge graph.

 Posted on March 31, 2022  |  Carsten

Introduction In this article, I will describe the steps taken to generate a RDF (Resource Description Format) datastructure starting from a gff3 formatted genome annotation file. The annotation file in question is the new reference annotation for Pseudomonas fluorescens strain SBW25. Required packages I will make use of the following python packages: gffutils to read the gff3 file into a sqlite database. rdflib to construct the rdf graph. requests to fetch data (e. [Read More]
RDF  Linked Data  Semantic Web  Knowledge Graph  genome annotation  Pseudomonas fluorescens  SBW25  gff  gff3