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Dr. Bruce A. Shapiro

We would like to hear from you about any installation and use problems, as well as no-problem experiences.

Suggestions and comments are always welcome. Please, contact Dr. Bruce A. Shapiro

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Requested Software

2017 VBox Virtual Machine: Ubuntu 14.04 LTS Linux, Galaxy server with NanoTiler tools, RNA2D3D 5.6.3 and StructureLab 4.7.0 installed (~5.0GB VM appliance file)

Local Galaxy server with NanoTiler tools pipeline is the most user-friendly version of this flexible RNA nanostructure building software. RNA2D3D is an interactive software package for the conversion of 2D RNA to 3D structures. First pass conversion is based on purely geometric criteria (idealized A-form helices). Following it, the user can interactively refine the structure via such features such as H-loop shaping, helix compactification, designated helix stacking, and substitution of structure subsets with known 3D motifs (PDB). Energy minimization and short molecular dynamics runs can be used for further refinements. StructureLab or SLab is an RNA/DNA Structure Analysis Workbench.

NEW: Built and tested in Oracle's VirtualBox 5.x on MS Windows 7 and Mac OSX 10.10 .. 10.12 host operating systems. The key advantage of this VM package is that all the non-trivial installation steps and dependencies on 64 bit and 32 bit libraries have been properly resolved.

Installation: 1) Download and install Oracle's free VirtualBox package from www.virtualbox.org. 2) In VirtualBox Manager window use File -> Import Appliance to load the appliance file with our software. 3) Start the virtual machine and login to RNALab with the password "RnaLab16". 4) After login, perform one-time installation of Guest System Additions: Devices -> Insert Guest Additions CD Image... and click OK in a dialog window. 5) Galaxy, RNA2D3D and SLab can be started by clicking on simple icons in the GNOME desktop. Open a console window to explore the app subdirectories under the home directory.

Oracle's free VirtualBox package is available from http://www.virtualbox.org.

2017 VBox Virtual Machine: CentOS 6.6 Linux, RNA2D3D 5.6.3, and StructureLab 4.7.0 installed (~2.0GB VM appliance file)

RNA2D3D is an interactive software package for the conversion of 2D RNA to 3D structures. First pass conversion is based on purely geometric criteria (idealized A-form helices). Following it, the user can interactively refine the structure via such features such as H-loop shaping, helix compactification, designated helix stacking, and substitution of structure subsets with known 3D motifs (PDB). Energy minimization and short molecular dynamics runs can be used for further refinements. StructureLab or SLab is an RNA/DNA Structure Analysis Workbench.

NEW: Built and tested in Oracle's VirtualBox 5.x on MS Windows 7 and Mac OSX 10.10 .. 10.12 host operating systems. The key advantage of this VM package is that all the dependencies on 64 bit and 32 bit libraries have been properly resolved. Once installed, CentOS 6.6 can be updated to version 6.9 Final.

Installation: 1) Download and install Oracle's free VirtualBox package from http://www.virtualbox.org. 2) In VirtualBox Manager window use File -> Import Appliance to load the appliance file with our software. 3) Start the virtual machine and login to RNALab with the password "adminuser". 4) After login, perform one-time installation of Guest System Additions: Devices -> Insert Guest Additions CD Image... and click OK in a dialog window. 5) RNA2D3D and SLab can be started by clicking on simple icons in the top GNOME window manager bar. Open a console window to explore the app subdirectories under the home directory.

Oracle's free VirtualBox package is available from http://www.virtualbox.org

RNA2D3D rev. 5.6.3, June 14, 2011. (Linux binary; OpenGL-based GUI, with links to Tinker)

RNA2D3D is an interactive software package for the conversion of 2D RNA to 3D structures. First pass conversion is based on purely geometric criteria (idealized A-form helices). Following it, the user can interactively refine the structure via such features such as H-loop shaping, helix compactification, designated helix stacking, and substitution of structure subsets with known 3D motifs (PDB). Energy minimization and short molecular dynamics runs relying on Tinker (automatically installed with kind permission of prof. J. Ponder) can be used for further refinements. Pseudoknots can be handled either automatically, or, if they are sterically very complicated, built interactively by the user. RNA2D3D can also be used to build RNA-based nano structures, such as tecto-squares and meshes (see Chworos et al.,Science 306, 2004). The system comes with a directory containing several sample structures (including pseudoknots and tecto-square building blocks) and offers help information dealing with the big picture issues as well as usage details.

NOTE: Despite the rev. number 5.6.3. this version is newer and more stable than the previously designated rev. 5.7 (different development path). Due to changes in the Tinker 5.x, which are incompatible with RNA2D3D (mid 2009), we temporarily include the previous version of Tinker binaries (v. 4.2) compatible with RNA2D3D, instead of a web download (wget) at the installation time. In response to user-raised issued we stamped out the known bugs in the code. PLEASE, keep in mind that this is a research software, and not an industrial strength package. Reference: Martinez, H., Maizel, J.V. Jr., and Shapiro, B.A. "RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA." J Biomol Struct Dyn. 2008 Jun;25(6):669-83.

Installation: 1) Download the distribution file. NOTE: Following step 2, a new subdirectory will be created. 2) Uncompress and extract the distribution files: tar -xzvf rna2d3d-file.gz 3) PLEASE, READ the RNA2D3D-README.txt file for the installation options. 4) Run C-shell (csh) script: CONFIG-RNA2D3D for the easiest installation. 5) Please, register your use of Tinker. 6) See the RNA2D3D-README.txt file for a step-by-step tectosqure building example.

RNA2D3D rev. 5.7.0, May 19, 2010. (SGI/Irix binary; OpenGL-based GUI, with links to Tinker)

This is the SGI MIPS / IRIX 6.5 version of the RNA2D3D package.

Installation: Same as for the Linux version.

NanoTiler v 0.11.1 , Jun 6. 2012. Java 6 application.

NanoTiler is a Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).

Installation: 1) Uncompress the tar file with: tar xfz nanotiler_v0.11.1_j6.tar.gz 2) Continue by following the installation instructions in nanotiler_v0.11.1/doc/NanoTilerUserManual.pdf

RSmatch2.0 - UNIX Version

The RSmatch package provides an approach to compare RNA structures, thereby uncovering functional structure elements. The software provides three different functions: 1) Pair-wise comparison and Database Search, 2) Multiple structure alignment with an extended mode to compute common structure, and 3) Iterative database search.

The Vienna RNA package must be installed if sequences written in the FASTA format are used. The Vienna RNA package can be downloaded at http://www.tbi.univie.ac.at/~ivo/RNA/. For more information, please see http://datalab.njit.edu/biodata/rna/RSmatch/software.htm.

RSmatch2.0 - WINDOWS Version

The RSmatch package provides an approach to compare RNA structures, thereby uncovering functional structure elements. The software provides three different functions: 1) Pair-wise comparison and Database Search, 2) Multiple structure alignment with an extended mode to compute common structure, and 3) Iterative database search.

For more information, please see http://datalab.njit.edu/biodata/rna/RSmatch/software.htm.

KNetFold rev. 1.4.4b (Linux binary)

KNetFold v 1.4.4b executable file for the Linux operating system. A software for predicting the concensus RNA secondary structure for a given alignment of nucleotide sequences.

CorreLogo v 1.2.6, Jan. 10, 2011.

A downloadable tar file contains souce files (C++) and 64-bit Linux binaries for the CorreLogo (same as our web server for the 3D sequence logos of RNA and DNA alignments).

Installation: 1) Uncompress the tar file with: tar -xfz correlogo_v1.2.6.tar.gz

CovaRNA (C++ sources) and CovStat (R package)

The CovaRNA and CovStat software packages for detecting long-range covariations in nucleotide alignments. This is the software corresponding to the publication of Bindewald and Shapiro: Computational deteaction of abundant nucleotide-covariation in Drosophila genomes. RNA, 2013.

Installation: unpack tar file with command tar xvfz covarna_1.16.0.tar.gz . Follow installation instructions in README file.

Intended Use of Software

License Agreement

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