nupack.org

NUPACK: Nucleic Acid Package

Is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. The NUPACK web application enables analysis and design of the equilibrium base-pairing properties of one or more test tubes of interacting nucleic acid strands:. The web application and algorithms appropriately; usage statistics are an important component in helping to secure funding for NUPACK development. We are happy to provide advice and technical support. Mdash; The NUPACK Team.

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NUPACK: Nucleic Acid Package | nupack.org Reviews

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Is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. The NUPACK web application enables analysis and design of the equilibrium base-pairing properties of one or more test tubes of interacting nucleic acid strands:. The web application and algorithms appropriately; usage statistics are an important component in helping to secure funding for NUPACK development. We are happy to provide advice and technical support. Mdash; The NUPACK Team.

<META> KEYWORDS

1 RNA

2 DNA

3 base pairing

4 secondary structure

5 folding

6 thermodynamics

7 design

8 prediction

9 minimum free energy

10 MFE

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analysis,design,utilities,downloads,nupack,please cite,news,supp info,source code,user guide,model,references,funding

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NUPACK: Nucleic Acid Package | nupack.org Reviews

https://nupack.org

Is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. The NUPACK web application enables analysis and design of the equilibrium base-pairing properties of one or more test tubes of interacting nucleic acid strands:. The web application and algorithms appropriately; usage statistics are an important component in helping to secure funding for NUPACK development. We are happy to provide advice and technical support. Mdash; The NUPACK Team.

INTERNAL PAGES

nupack.org

1

NUPACK: Utilities

http://www.nupack.org/utilities

Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed. Enter the temperature (default 37 °C). Update all calculations and graphics. Specify a secondary structure in dot-parens-plus notation (each unpaired base is represented by a dot, each base pair by matching parentheses, and each nick between strands by a plus). Structures must be connected and free of pseudoknots. For example:. Use the MFE structure as the specified structure. Position of the cursor within the ordered complex.

2

NUPACK: Downloads

http://www.nupack.org/downloads

You are welcome to download NUPACK source code for non-commercial academic purposes. Please register. To sign a license agreement and obtain a download password. Enjoy the software! Mdash; The NUPACK Team.

3

NUPACK: Funding

http://www.nupack.org/home/funding

The National Science Foundation. Via the Molecular Programming Project. The Beckman Institute at Caltech. Via the Programmable Molecular Technology Center. The Gordon and Betty Moore Foundation.

4

NUPACK: Model

http://www.nupack.org/home/model

NUPACK algorithms are formulated in terms of nucleic acid secondary structure. The. Of one or more interacting nucleic acid strands is defined by a list of base pairs (Dirks et al., 2007). A. Representation of a secondary structure is constructed by ordering the strands around a circle, drawing the backbones in succession from 5’ to 3’ around the circumference with a. Between each strand, and drawing straight lines connecting paired bases. A secondary structure is. SantaLucia and Hicks, 2004; Koehler and...

5

NUPACK: References

http://www.nupack.org/home/references

J N Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, N. A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem. 32:170 173, 2011. ( pdf. R M Dirks, J. S. Bois, J. M. Schaeffer, E. Winfree, and N. A. Pierce. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev. 49:65-88, 2007. ( pdf. R M Dirks and N. A. Pierce. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem.

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itToby: July 2014

http://blog.ittoby.com/2014_07_01_archive.html

Because if I don't write it down I might forget it. Wednesday, July 30, 2014. Why Schannel EventID 36888 / 36874 Occurs and How to Fix It. Having trouble talking to your webserver? Seeing the aforementioned errors? I can fix two of those. I ran into this error at a large, highly distributed client site. Because of the nature of the problem (sporadic) it took longer to solve than I would have liked. Hopefully this article will save you that time. What Components are Involved? How to verify the message has...

rnavlab.utep.edu

RNAVLab for Bioinformatics Analysis

http://rnavlab.utep.edu/rnavlab/downloads.php

RNAVLab for Bioinformatics Analysis. Ribonucleic Acid Virtual Laboratory for Sequence Analysis, Structure Prediction, and Databases. RNAVLab, Example Input Files, and MySQL Table. Download and installation instructions:. RNAVLab class files, MySQL example table, and example input files:. With RNA Segmentation and Assembly:. RNASSA 2.0.150128 (zip file; Java and R required). A Bioinformatics Tool for RNA Segmentation:. Segmenta 2.0.150303 (zip file; Java and R required). For developing Java applications:.

molecular-programming.org

MPP: Home

http://molecular-programming.org/MPP.html

An Expedition in Computing. Funded by the National Science Foundation. An Expedition in Computing. Funded by the National Science Foundation. Optical imaging of individual biomolecules in densely packed clusters. Jul 4, 2016. Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing. Jun 25, 2016. Multiplexed miRNA northern blots via hybridization chain reaction. Jun 8, 2016. May 19, 2016. May 6, 2016. Digital computation with DNA. Dai M et al.

commofc.eas.caltech.edu

E&AS Communications Office - Websites

http://commofc.eas.caltech.edu/websites.html

Website Design and Development. Ruby on Rails Development. Divison of Engineering and Applied Science. The Keck Institute for Space Studies (KISS). The Kavli Nanoscience Institute (KNI). Information Science and Technology. Center for Bioinspired Engineering. Southern California Earthquake Data Center. Caltech Center for Sustainable Energy Research. Joint Center for Translational Medicine. Center of Excellence in Genomic Science. Center for the Mathematics of Information. Mechanical and Civil Engineering.

yanlab.asu.edu

Yan Lab Resources

http://yanlab.asu.edu/Resources.html

In collaboration with Sean Williams (Programmer, now at UC Davis), Peter Wonka (ASU) and Stuart Lindsay (ASU), we developed a graphical user interface program for the design of DNA nanostructures and sequences. Please click to download this program. And a user manual. DNA models created by Tiamat (.dna files): Double crossover (DAE) tile. Catoons animated using Tiamat (.avi files): 4x4 tile. By Michael Zuker at Rensselaer Polytechnic Institute. By Niles Pierce and Colleagues at Caltech.

piercelab.caltech.edu

The Pierce Lab - Caltech - Resources

http://piercelab.caltech.edu/resources

California Institute of Technology. Is a growing software suite for the analysis and design of nucleic acid molecules, devices, and systems. Is a non-profit academic resource dedicated to the development and support of programmable molecular instruments for reading out and regulating the state of endogenous biological circuitry within intact organisms. 2015 • Contact.

molecular-programming.org

MPP: Software

http://molecular-programming.org/software.html

An Expedition in Computing. Funded by the National Science Foundation. An Expedition in Computing. Funded by the National Science Foundation. Optical imaging of individual biomolecules in densely packed clusters. Jul 4, 2016. Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing. Jun 25, 2016. Multiplexed miRNA northern blots via hybridization chain reaction. Jun 8, 2016. May 19, 2016. May 6, 2016. DNA Strand Displacement tool. UW Center for Sy...

eternawiki.org

Computational Tools - EteRNA WiKi

http://eternawiki.org/wiki/index.php5/Computational_Tools

Cloud Lab Data Mining Tool. Computationally Selected Elements (CSE). Http:/ rna.tbi.univie.ac.at/. Http:/ www.tbi.univie.ac.at/ ronny/RNA/index.html. Http:/ en.wikipedia.org/wiki/List of RNA structure prediction software. Quickguide to Vienna RNA fold. Http:/ varna.lri.fr/. Http:/ www.cgl.ucsf.edu/chimera/. Http:/ www.cgl.ucsf.edu/chimera/download.html. Cloud Lab Data Mining Tool. Lab data analysis tool made by Omei. For more about how to use the tool, it see the manual here. For a lab data analysis tool...

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nupachi | DeviantArt

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nupack.org

NUPACK: Nucleic Acid Package

Is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. The NUPACK web application enables analysis and design of the equilibrium base-pairing properties of one or more test tubes of interacting nucleic acid strands:. The web application and algorithms appropriately; usage statistics are an important component in helping to secure funding for NUPACK development. We are happy to provide advice and technical support. Mdash; The NUPACK Team.

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Home | NU Packaging, Inc.

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NuGet Packages - Home

Project Hosting for Open Source Software. By clicking Delete, all history, comments and attachments for this page will be deleted and cannot be restored. Change History (all pages). This site is now obsolete! Please use http:/ nuget.org. To submit packages now! Old content follows, only for reference. Welcome to the temporary NuGet package repository site. This is a temporary repository for NuGet. Here is what you need to do to contribute packages:. Fork the nupackpackages repository. See all this page.

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