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Ascend, Owens, Pitzer
Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. Nextflow is based on the dataflow programming model which simplifies complex distributed pipelines.
Ascend, Cardinal, Owens, Pitzer
Nodejs is used to create server-side web applications, and it is perfect for data-intensive applications since it uses an asynchronous, event-driven model
SUG Mini Meeting - Oct. 17, 2023
OSC Updates
Owens, Pitzer
GPU Usage on Tensorflow
Environment Setup
To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create Python Environment for more details. In this example we are using python/3.6-conda5.2
Ascend, Owens, Pitzer
We can improve performace of python calculation by running python in parallel. In this turtorial we will be making use of the multithreading library to run python code in parallel.
Owens, Pitzer
If you plan on using GPUs in tensorflow or pytorch see HOWTO: Use GPU with Tensorflow and PyTorch
This is an exmaple to utilize a GPU to improve performace in our python computations. We will make use of the Numba python library. Numba provides numerious tools to improve perfromace of your python code including GPU support.
Owens, Pitzer
Mathematica is a mathematical computation program. It is capable in many areas of technical computing including but not limited to neural networks, machine learning, image processing, geometry, data science and visualizations.
Owens, Pitzer
Tinker is a molecular modeling package. Tinker provides a general set of tools for molecular mechanics and molecular dynamics.
Cardinal, Pitzer
MRIcroGL is medical image viewer that allows you to load overlays (e.g. statistical maps), draw regions of interest (e.g. create lesion maps).
Availability and Restrictions
Versions
MRIcroGL is available on Pitzer cluster. These are the versions currently available:
Cardinal, Pitzer
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices).
