D2CMA 0.1 – Design 2 Color MicroArrays

D2CMA 0.1

:: DESCRIPTION

D2CMA contains a few R-scripts, mainly the function optimize.MA.design which builds upon the daMA package. It was used to optimize the two-color microarray experimental design for analyzing the differential responses of sensitive and tolerant rice cultivars to drought stress

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 D2CMA

:: MORE INFORMATION

AutoGrow 4 – Use AutoDock Vina in Protein Inhibitor Design

AutoGrow 4

:: DESCRIPTION

AutoGrow (Java DOCK), uses fragment-based growing, docking, and evolutionary techniques.Due in part to the increasing availability of crystallographic protein structures as well as rapid improvements in computer power, the past few decades have seen an explosion in the field of computer-based rational drug design. Several algorithms have been developed to identify or generate potential ligands in silico by optimizing the ligand-receptor hydrogen bond, electrostatic, and hydrophobic interactions.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AutoGrow

:: MORE INFORMATION

Citation

J Mol Graph Model, 44, 104-12 Jul 2013
AutoGrow 3.0: An Improved Algorithm for Chemically Tractable, Semi-Automated Protein Inhibitor Design
Jacob D Durrant , Steffen Lindert, J Andrew McCammon

Durrant, J. D.; Amaro, R. E.; McCammon, J. A. 2009.
AutoGrow: A Novel Algorithm for Protein Inhibitor Design
Chemical Biology & Drug Design. 73(2):168-78.

OligoWiz 2.3.1 – Design oligonucleotides for DNA microarrays

OligoWiz 2.3.1

:: DESCRIPTION

OligoWiz performs intelligent design of oligonucleotides for DNA microarrays. It is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (written in Java) which delegates the computationally intensive operations to a powerful Multi-CPU server hosted at the Center for Biological Sequence Analysis.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / UNIX / MacOS X
  • Java

:: DOWNLOAD

OligoWiz Client

:: MORE INFORMATION

Citation

OligoWiz 2.0 – integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496

MODEST 0.1.4-10 – MAGE Oligo Design Tool

MODEST 0.1.4-10

:: DESCRIPTION

MODEST allows the rapid and effective design of optimal MAGE (multiplex automated genome engineering) oligos based on simple input, to achieve any mutation possible with MAGE.

::DEVELOPER

Wang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Bonde MT, Klausen MS, Anderson MV, Wallin AI, Wang HH, Sommer MO.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W408-15. doi: 10.1093/nar/gku428

CellBlender 3.5.0 – Blender addon for Creation, Simulation, Visualization, and analysis of 3D Cell Models

CellBlender 3.5.0

:: DESCRIPTION

CellBlender is an addon for Blender-2.6x to create computational cell biology models for use in MCell and potentially other cell simulation biophysics engines. In CellBlender 0.49 you can create geometric objects, assign surface regions to said objects, export the objects as MCell MDL geometry files, set MCell simulation parameters, import a time-series of MCell VIZ_OUTPUT, and interactively playback or render an animation of the VIZ_OUTPUT. MDL import along with other features will be added in future versions.

CellBlender is replacing PSC_DX and DReAMM as the primary tool to visualize MCell simulations.

::DEVELOPER

The National Center for Multiscale Modeling of Biological Systems (MMBioS)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 CellBlender

:: MORE INFORMATION

Citation:

Stiles, JR, and Bartol, TM. (2001).
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell.
In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127.

BioJazz – Evolve and Design Biochemical Reaction Networks

BioJazz

:: DESCRIPTION

BioJazz is a tool for evolving and designing biochemical reaction networks using genetic algorithm (GA).

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Matlab

:: DOWNLOAD

 BioJazz

:: MORE INFORMATION

Citation

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.
Feng S, Ollivier JF, Swain PS, Soyer OS.
Nucleic Acids Res. 2015 Jun 22. pii: gkv595.

STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Staden

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

PrimerProspector 1.0.1 – Design and Analyze PCR Primers

PrimerProspector 1.0.1

:: DESCRIPTION

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • PyCogent
  • Numpy
  • Matplotlib

:: DOWNLOAD

 PrimerProspector

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087.
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

BOND – Basic OligoNucleotide Design

BOND

:: DESCRIPTION

BOND is a program for designing DNA oligonucleotides. In comprehensive testing, it achieved 100% sensitivity and specificity.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BOND

:: MORE INFORMATION

Citation

BOND: Basic OligoNucleotide Design.
Ilie L, Mohamadi H, Golding GB, Smyth WF.
BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.