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Tools

Rothbart Laboratory

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.

More Information

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

brd4_smallOverview

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

The Histone Antibody Specificity Database

tools_histonedatabaseOverview

Access to high-quality antibodies is a necessity for the study of histones and their posttranslational modifications (PTMs). The Histone Antibody Specificity Database is an online and expanding resource that catalogs the behavior of widely used, commercially available histone antibodies by peptide microarray. This interactive web portal provides a critical resource to the biological research community that routinely uses these antibodies as detection reagents for a wide range of applications.

Access the database 

More Information

Contact

scott.rothbart@vai.org

Citations

Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenberg AJ, Strahl BD. 2015. An interactive database for the assessment of histone antibody specificity. Molecular Cell 59(3):502–511.

Publications

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB. In press.  ArrayNinja: An open source platform for unified planning and analysis of microarray experiments. Methods Enzymol.

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB. In press. Substrate specificity profiling of histone-modifying enzymes by peptide microarray. Methods Enzymol.

Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenberg AJ, Strahl BD. 2015. An interactive database for the assessment of histone antibody specificity. Molecular Cell 59(3):502–511.