Skills

Our team¡¯s software skills span a broad range of

• programming languages (e.g. Java, Python, Julia, C++, Matlab)
• extendable applications (e.g. Fiji, Napari, BigDataViewer, Neuroglancer)
• frameworks (e.g. NumPy/SciPy, ImgLib2, PyTorch, Spark, Dask)
• cloud & cluster technologies (e.g. storage and distributed compute on Amazon Web Services, Google Cloud & Janelia cluster, containerization)
• databases (e.g. MySQL, MongoDB).

In addition to software skills, our team has deep domain knowledge in image processing, machine learning, (large) data handling, electron and light microscopy, instrument control, 3D graphics & visualization as well as bioformatics & transcriptomics and many of us have worked in biology, so we can efficiently work with experimentalists and computer scientists! Almost half of our team members have earned PhDs, in areas including computer engineering, electrical engineering, physics, biology, biochemistry, and computational neuroscience. To have an overview and/or find a good person to talk to we maintain a skills matrix available to internal users.

Our Goals

It is very important for us to identify opportunities for code reuse, reducing development overhead and support costs across Janelia. To achieve this we are strong proponents of open science and for example teamed up with the Computation & Theory research area (C&T) to create the Open Science Software Initiative. Additionally, most of our software is open source and available via GitHub.

We strive to be an active part of Janelia's scientific community and you will see us attending presentations and interest groups. Additionally, SciComp holds weekly office hours. We also have a series of Scientific Computing Interest Groups that are open to all Janelians. Most interest groups are recorded and can be accessed through Panopto internally, while some of them are publicly available on our YouTube channel.

We are looking forward to working with you!

Organization / Structure of SciComp Software

The director of SciComp is Stephan Preibisch and it consists of three teams: Software Engineering headed by Konrad Rokicki, Software Solutions, headed by Stuart Berg; and Computational Methods headed by Stephan Preibisch.

Each team conducts its own internal meetings. The entire group attends SciComp team meetings, during which the science discussions are open to interested parties.

SciComp organizes the Scientific Computing Associate (SCA) program that embeds SCA's in SciComp and the lab or team they work with. The Scientific Computing Interest Groups are run by SciComp engineers and SCA's. The Open Science Software Initiative is a collaboration between C&T and SciComp.