XSEDE Software Discovery

This image has Docker and gsissh installed
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/880
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

This contains the base webpage, R packages, sample database on postgresql, and documentation for collecting data from Raspberry Pi recording devices
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/857
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Ubuntu 18.04 LTS + Xfce desktop, Anaconda Python 3.7
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/781
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Current Iteration of JBrowse image end of april 2019
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/840
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Friday 8 March 2019
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/826
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Explicit Planetary Isentropic-Coordinate (EPIC) Atmospheric Model
Based on Ubuntu 14.04.3 Development
Patched up to date as of 1/2/17
Base Ubuntu 14.04.3 + Xfce + Xfce-goodies, firefox, icon sets and themes
EPIC 3v9
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/100
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

EDGE bioinformatics website
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/808
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Centos7 GUI development with Agisoft's photoscan preinstalled and configured
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/789
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/752
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Loaded with LAMP stack and Drupal with up to date security patches.
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/739
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Based on Ubuntu 18.04 devel and docker, with bioconda added.
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/736
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/722
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

updates Bioc packages and includes HSOS infrastructure of Dec 2017
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/669
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Anaconda python 3.6, OpenMM
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/663
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

This image is intended for Genome annotation using MAKER using cctools (WQ-MAKER)
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/492
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Adding infrastructure to support running hdf server.
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/588
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Includes sufficient infrastructure to run rhdf5client + HSOS
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/579
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Includes sufficient infrastructure to run rhdf5client
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/508
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Common packages for phylogenetics, population genetics, and phylogeography. Type "module avail" to view installed modules.
View this image in Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/145
Discover more images using Jetstream Atmosphere: https://use.jetstream-cloud.org/application/images/search
Jetstream Getting Started Guide: https://wiki.jetstream-cloud.org/Quick+Start+Guide
Introduction to Jetstream Workshop: https://cvw.cac.cornell.edu/jetstream/

Globus Toolkit GridFTP Services
Vendor Software URL: http://toolkit.globus.org/toolkit/data/gridftp/

XSEDE Information Services (IS)
Vendor Software URL: https://info.xsede.org/

Genesis II distributed computing platform
Vendor Software URL: http://genesis2.virginia.edu/wiki/Main/HomePage

Kerberos is a network authentication protocol. It is designed to provide strong authentication for client/server applications by using secret-key cryptography. A free implementation of this protocol is available from the Massachusetts Institute of Technology. Kerberos is available in many commercial products as well.
Vendor Software URL: https://web.mit.edu/kerberos/

MyProxy is open source software for managing X.509 Public Key Infrastructure (PKI) security credentials (certificates and private keys). MyProxy combines an online credential repository with an online certificate authority to allow users to securely obtain credentials when and where needed. Users run myproxy-logon to authenticate and obtain credentials, including trusted CA certificates and Certificate Revocation Lists (CRLs).
Storing credentials in a MyProxy repository allows users to easily obtain RFC 3820 proxy credentials, without worrying about managing private key and certificate files. They can use MyProxy to delegate credentials to services acting on their behalf (like a grid portal) by storing credentials in the MyProxy repository and sending the MyProxy passphrase to the service. They can also use MyProxy to renew their credentials, so, for example, long-running jobs don't fail because of expired credentials. A professionally managed MyProxy server can provide a more secure storage location for private keys than typical end-user systems. MyProxy can be configured to encrypt all private keys in the repository with user-chosen passphrases, with server-enforced policies for passphrase quality. By using a proxy credential delegation protocol, MyProxy allows users to obtain proxy credentials when needed without ever transferring private keys over the network.
For users that don't already have PKI credentials, the MyProxy Certificate Authority (CA) provides a convenient method for obtaining them. The MyProxy CA issues short-lived session credentials to authenticated users. The repository and CA functionality can be combined in one service or can be used separately.
MyProxy provides a set of flexible authentication and authorization mechanisms for controlling access to credentials. Server-wide policies allow the MyProxy administrator to control how credentials may be used. Per-credential policies provide additional controls for credential owners. MyProxy supports multiple authentication mechanisms, including passphrase, certificate, Kerberos, OAuth, SAML, OpenID, Pubcookie, VOMS, PAM, LDAP, RADIUS, SASL, Moonshot, and One Time Passwords (OTP).
Vendor Software URL: http://grid.ncsa.illinois.edu/myproxy/oauth/

Molecular mechanical force fields for the simulation of biomolecules and package of molecular simulation programs
Vendor Software URL: http://ambermd.org/