Tools

ArrayNinja

TOOLS_ArrayNinja_200x200Overview

ArrayNinja is a portable, open source and interactive application that unifies the planning, visualization, and analysis of custom microarray experiments.

ArrayNinja is distributed as a virtual machine (VM) that runs a local and private web server. Because the tools are packaged as a VM and utilize a web browser as a user interface, ArrayNinja is platform agnostic.

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Download and installation

Virtual Machine
The ArrayNinja VM is built to use VirtualBox, which is a free tool for building and running virtual machines. VirtualBox must be installed before the ArrayNinja VM can be used.

To download the ArrayNinja VM, visit http://research.vai.org/Tools/arrayninja/

To run ArrayNinja, unzip the VM and load the VM into virtualbox. Once the VM is running, navigate your web browser to http://localhost:2080

Docker Application
ArrayNinja can be run on linux platforms via a docker application. The docker can be found at Docker Hub and it can be installed by pulling bradleydickson/arrayninja.

The docker app should be started with command:
docker run -d -p 2080:80 bradleydickson/arrayninja

License

Academic and not-for-profit
ArrayNinja is released under GNU General Public License, version 2. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Contact

For business and licensing inquiries, please contact BusinessDev@vai.org.
For scientific inquiries, please contact inquiries@arrayninja.com.

Citations

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB. 2016. ArrayNinja: ArrayNinja: An open source platform for unified planning and analysis of microarray experiments. Methods Enzymol 574:53–57.

Publications

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB. 2016. ArrayNinja: ArrayNinja: An open source platform for unified planning and analysis of microarray experiments. Methods Enzymol 574:53–57.

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB. 2016. Substrate specificity profiling of histone-modifying enzymes by peptide microarray. Methods Enzymol 574:31–52.

fABMACS


Overview

fABMACS is a flexible adaptively biased flavor of GROMACSv5.0.5. fABMACS was developed to maximize scalability of adaptive biasing so that better efficiency can be achieved when simulation systems are distributed across a large computing infrastructure.

More Information

Download and installation

fABMACS is available for download and use. Instructions and example inputs (for the ligand-protein system in the publication) are available as well. Please visit https://github.com/BradleyDickson/fABMACS.

License

Academic and not-for-profit
fABMACS is released under GNU General Public License, version 2. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Contact

For questions about fABMACS or commercial use, contact bradley.dickson@vai.org.

Citations

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. In press. A fast, open source implementation of adaptive biasing potential uncovers a ligand design strategy from the chromatin regulator BRD4. J Chem Phys.       Article