SOFTWARE DOWNLOADS

Vbox appliance files (virtual machine archives) have been built and tested in Oracle's VirtualBox 5.x and 6.x under MS Windows 10 and MacOS 10.10 .. 11.5 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. Note: We have recently noticed that older VBox versions (6.0.x, up to 6.1.2) are more stable than the latest releases. Under MacOS newer VBox versions experience a memory leak that blows the rquested amount of VM RAM)

Pre-installed Software: 


Installation: 

  1. Download and install Oracle's free VirtualBox and a matching Oracle_VM_VirtualBox_Extension_Pack packages from http://www.virtualbox.org and install them in that order. 
  2. In VirtualBox Manager window use File -> Import Appliance to load the appliance file with our software. 
  3. In VirtualBox Manager review the system hardware Settings and the mount point of the host machine file system in the VM (Settings -> Shared Folder).
  4. Important Note: The key VM setting that need to be adjusted to your hardware involve Settings -> Display/Graphics Controller (VMSVGA vs VBoxSVGA) and Display/3D acceleration. Experiment with these setting, if you experience suboptimal graphics or app crashes.
  5. Start the virtual machine and login to to host named RNALab or rnalab with the password "RnaLab16" for Ubuntu 14, or "RnaLab20" for Ubuntu 18, Ubuntu 20, and for CentOS. Ubuntu admin pass is the same as user login pass, while CentOS admin pass is $adminuser$.  
  6. After login, CHANGE YOUR PASSWORD ASAP and perform one-time installation of Guest System Additions: Devices -> Insert Guest Additions CD Image... click OK in a dialog window. Also, install all OS (CentOS/Ubuntu) system updates via Admin Tools Menu. Reboot the VM for the changes to take effect. 
  7. Start the web browser to display information about the installed software packages. Galaxy, RNA2D3D and SLab can be started by clicking on simple icons in the GNOME desktop or via System Applications Menus (If necessary, login to the Galaxy server as guest@rna.lab/password). Open a console window to explore the app subdirectories under the home directory.


============================================================

Ubuntu 20.04LTS, kernel 5.4 (64 bit) with MPGAfold. Oct 07, 2020 (5.9 GB)

VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold (Genetic Algorithm for RNA/DNA secondary structure prediction) installed. Note: no Galaxy/NanoTiler installed.

Ubuntu 18.04LTS, kernel 4.15 (64 bit) with MPGAfold. Oct 07, 2020 (5.5 GB)

VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold (Genetic Algorithm for RNA/DNA secondary structure prediction) installed. Note: no Galaxy/NanoTiler installed.

Ubuntu 18.04LTS, kernel 4.15 (64 bit). Mar 13, 2019 (3.3 GB)

VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, and StructureLab installed. Note: no Galaxy/NanoTiler installed.

Ubuntu 14.04LTS, kernel 4.4 (64 bit). Update: Oct 20, 2020 (3.5 GB)

VBox Virtual Machine appliance file (OVA) with Galaxy/NanoTiler, RiboSketch, RNA_2D3D, and StructureLab installed.

CentOS 7.7 (64bit) with MPGAfold. Aug 03, 2021 (2.9 GB)

VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold with Visualizer (Genetic Algorithm for RNA/DNA secondary structure prediction and GUI module) installed.

CentOS 6.10 (64bit). Oct 11, 2018 (2.2 GB)

VBox Virtual Machine appliance file (OVA) with RNA_2D3D and StructureLab installed.


============================================================

RiboSketch (2018)

RiboSketch is a drawing program for the production of single or multi-stranded RNA and DNA secondary structure images. Multiple strands (chains), non-canonical interactions, hybrid RNA-DNA base-pairing, pseudoknots, and interstrand interactions are supported. Circle diagams and other layout options are available, utilizing dynamic simulation mode (automatic "relaxed" layout) and/or fully interactive editing. 

Installation: See the RiboSketch Web Page for details 


============================================================

RNA2D3D 5.6.3 (Linux binary)

RNA2D3D (Linux binary, Open-GL GUI, links to Tinker for energy minimization) 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 geometrically 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.

Installation: 

1) Download, uncompress and extract the distribution files: tar -xzvf rna2d3d-file.gz Note: A new subdirectory will be created. 

2) PLEASE, DO READ the RNA2D3D-README.txt file for the installation options. 

3) Run C-shell (csh) script: CONFIG-RNA2D3D for the easiest installation. 

4) See the RNA2D3D-README.txt file for a step-by-step tectosqure building example. 

5) Please, register your use of Tinker.


Note: Revision 5.6.3. is newer and more stable than the previously designated rev. 5.7 (different development path). 

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.


RNA2D3D 5.7.0 (Irix 6.5 binary for SGI MIPS platform)


============================================================

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 and extract the tar file: tar -xfz nanotiler_v0.11.1_j6.tar.gz 

2) Follow the installation instructions from nanotiler_v0.11.1/doc/NanoTilerUserManual.pdf


============================================================

KNetFold rev. 1.4.4b (Linux binary)

A software for predicting the concensus RNA secondary structure for a given alignment of nucleotide sequences. 

Alternatively, try the KNetFold Web Server


============================================================

RSmatch2.0 (Linux binary)

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. 

Note: 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 binary)


============================================================

CorreLogo 1.2.6 (Jan 10, 2011) (Linux binary & sources)

The 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) Download, uncompress and extract the distribution files: tar -xfz correlogo_v1.2.6.tar.gz 


Alternatively, try the CorreLogo Web Server


============================================================

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

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

Installation: 

1) Download, uncompress and extract the distribution files: tar -xvfz covarna_1.16.0.tar.gz 

2) Follow installation instructions from the README file.


============================================================


Contact: Wojciech (Voytek) K. Kasprzak, kasprzaw@nih.gov 

Last revision: April 20, 2021

============================================================