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Pitzer

MotionCor2 uses multi-GPU acceleration to correct anisotropic cryo-electron microscopy images at the single pixel level across the whole frame, making it suitable for single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

Gateway

MyOSC now offers the ability for PIs to view the billing statements of current un-billed usage for their projects.

Login to my.osc.edu and navigate to Project -> Billing Statements.

There are two sections:

Current usage

The current usage section provides information usage charges up to the current day.

Keep protected data in proper locations

Protected data must be stored in predetermined locations. The only locations at OSC to store protected data are /fs/ess/<project-code> and /fs/ess/scratch/<project-code> directories.

SUG Conference - October 7, 2021

Agenda

Owens, Pitzer

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes.

 

Owens, Pitzer

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMS). HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models.

Pitzer

AlphaFold is a software package that provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and pusblished in Nature.

Owens, Pitzer

The IPython kernel for a Conda/virtual environment* must be installed on Jupyter prior to use.

Owens, Pitzer

TeX Live is a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro pacakges, and fonts that are free software, including support for many languages around the world.

Owens, Pitzer

JupyterLab stores the main build of JupyterLab with associated data, including extensions in Application Directory. The default Application Directory is the JupyterLab installation directory where is read-only for OSC users. Unlike Jupyter Notebook, JupyterLab cannot accommodate multiple paths for extensions management.

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