Scientific Computing
The Scientific Computing Software staff have technical skill sets that include expertise in Java, C/C++, Python, PERL, MATLAB, MySQL databases and web design. Members of the department also have domain backgrounds in bioinformatics, electron microscopy, Instrument control, large software systems/data management, 2D and 3D Data visualization, and human/computer interfaces. Nine department members possess Ph.D.s in subjects such as computer engineering, electrical engineering, physics, neurobiology, biochemistry and computational neuroscience.
The department has produced software for visualization and 3-D rendering of neural circuits, data acquisition and control of microscopes and other instruments, and multi-user proofreading of segmentation algorithms for large electron microscopy datasets. Staff have also created systems to index and annotate image collections with over one million images, and pipelines for generation of secondary images running on the cluster to support analysis. One of the most recent projects involved building a simulated virtual maze for rodents, allowing for extremely large or physically impossible mazes.
The department has worked on a large range of project types. Some researchers simply ask for advice and guidance. Others have brought with them partial or dated codebases that require augmentation to support their research. Many projects have been greenfield development, starting from scratch on a new problem. Projects have ranged from several days to multiple years in duration. In many regards, the department is not only able to learn the scientific details necessary to effectively develop software, but it can also offer assistance in planning and development of an experiment. Additionally the department is positioned to see synergies in efforts between multiple labs that can lead to collaborations or, at least, reuse of existing software systems to reduce development time and cost.







