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Owens, Pitzer
CIAO (also known as Chandra Interactive Analysis of Observations) is a X-Ray telescope analysis software package for astronomical observation. CIAO focuses on the Chandra X-ray observatory. It contains a toolset used to analyze fits files and is commonly used in conjuction with DS9 and Sherpa, and focuses on data flexibility.
Owens, Pitzer
SAOImageDS9 is a astronomical imaging and data visualization application. DS9 provides support for FITS images, binary tables, multiple frame buffers, region manipulation, and colormaps display options
Availability and Restrictions
The following versions of DS9 are available on OSC clusters:
Owens, Pitzer
WCStools is a program package designed for working with Images and the World Coordinate System. The aim of WCStools is to provide methods for relating pixels taken common astronomical images to sky coordinates.
Availability and Restrictions
The following versions of WCStools are available on OSC clusters:
Pitzer
Cell Ranger is a cell analysis library for generate feature-barcode matrices, perform Analysis for RNA samples. Cell Ranger works in pipelines for it's RNA sequencing analysis which allows it to: process raw sequencing output, read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis.
SUG Conference - October 7, 2021
Agenda
Gateway, Owens, Pitzer
Add to a Classroom Project
We provide the instructor (PI of the classroom project) with information on how to get students added to the classroom project. Usually, invites will be sent to new OSC users; existing OSC users will be automatically added to the project if they have an OSC account which matches the email information provided by the PI.
SUG Conference - April 14, 2021
Agenda
The data transfer speed between OSC and another network can be tested.
Test data transfer speed with iperf3 tool
Connect to a data mover host at osc and note the hostname.
$ ssh sftp.osc.edu # login $ hostname datamover02.hpc.osc.edu # the hostname may also be datamover01.hpc.osc.edu
From there, an iperf3 server process can be started. Note the port used.
Pitzer
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurrig due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format. Unblur generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages. Movie frame sums can also be calculated using Summovie, which uses the alignment resuls from a prior run of Unblur.