Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested to implement a process involving Python packages from a paper published in 2019: “AlleleAnalyzer: a tool for personalized and allele-specific …
Summary sandbox.bio provides interactive tutorials for exploring bioinformatics command-line tools within a web browser. Bioinformatics When people ask “what is bioinformatics” I have to pause. When I named a computer “bioinformatics” at the dawn of the Internet Age (1994) it made sense to me base on the French language: “informatique” is a French word for …
Summary A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large sample files. Docker on Biochemistry Compute Cluster The HTCondor scheduler software on the Biochemistry Compute Cluster (BCC) can run Docker …
Programming for Biology 2019 The famous Cold Spring Harbor Laboratory offers many courses, the course Programming for Biology 2019 was held in October 2019 and this specific course generously offers the course materials online on this site: programmingforbiology.org The course materials covers basics and advanced methods using Unix & Python and provides tutorial materials that include …