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Please use https://code.google.com/p/ganymed-ssh-2/ , as this current project is not getting the attention it should and therefore should be considered as 'parked'.
Orion SSH for Java is a library which implements the SSH-2 protocol in pure Java. This is the new name, and home, for Trilead SSH (formerly Ganymed SSH2).
jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
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MuleDesigner is an extension of Publisher Subscriber model intended to be used by telecommunication industry as a flexible code generated billing mediation system and ESB for JBoss . Currently the supported protocols are Telnet, FTP, SSH, HTTP,SMPP.
A simple CVS client that bypass any firewall blocking port 2401 used by cvs. It relies on the ViewCVS web interface to the repository to work. To use when all other solutions (SSH...) fail
BatchSSH (or just bssh) is a command line tool for batch execution of commands over SSHv2. BatchSSH is implemented in Java and is therefore platform agnostic. It support's simple but flexible target host definition, SSH gateways and Single-Sign-On.
Deployer is an Eclipse plug-in to deploy files in remote servers, using SSH. It's written in Java and released under the LGPL. It adds a Preferences page to the resources to set the deployment information, and a submenu with a Deploy action.
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Gruntspud is a graphical CVS client written in Java. It supports a variety of different connection mechanisms (local, pserver, ext, ssh & server). It is intended to be able to run as a plugin to jEdit but also as as a standalone application.
A fast and flexible implementation of SSH and SCP for Java, modelled on OpenSSH. In the beginning it should be simple, but hopefully eventually feature-rich.