SAT 1.2 – Sequence Alignment Teacher

SAT 1.2

:: DESCRIPTION

SAT is a software to teach about sequence alignment methods based on dynamic programming such as Smith – Waterman (Local) and Needleman – Wunsch (Global).

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SAT

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 1;26(13):1664-5. doi: 10.1093/bioinformatics/btq252. Epub 2010 May 14.
Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.
Ibarra IL1, Melo F.

eteRNA / NOVA RNA VirtuaLab – RNA Game Lets Players Help Find a Biological Prize

eteRNA / NOVA RNA VirtuaLab

:: DESCRIPTION

By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science.

In NOVA RNA VirtuaLab you’ll play the role of a molecular engineer by solving RNA folding puzzles. Then take your skills to Eterna, where you can design RNAs that could be at the heart of future life-saving therapies.

::DEVELOPER

the Das Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser
  • Flash

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

JOHN MARKOFF
RNA Game Lets Players Help Find a Biological Prize
The New York Times January 11, 2011, on page D4

Virtual Ribosome 2.0 / dna2pep 1.1 – Translating DNA sequences to the corresponding Peptide Sequences

Virtual Ribosome 2.0 / dna2pep 1.1

:: DESCRIPTION

The Virtual Ribosome (dna2pep) is a comprehensive tool for translating DNA sequences to the corresponding peptide sequences.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

  dna2pep

:: MORE INFORMATION

Citation

Virtual Ribosome – a comprehensive translation tool with support for sequence feature integration.
Rasmus Wernersson.
Nucl. Acids Res. 2006 34: W385-W388

DNA-Crypt 2.1 – Encrypts files into DNA Sequences

DNA-Crypt 2.1

:: DESCRIPTION

DNA-Crypt is a cryptography tool which encrypts files into DNA sequences. These sequences can be transfered to bacteria or other organisms without influencing them. You can use cryptographic keys, like RSA, AES or Blowfish, or, for maximum security, you can use a one time pad with DNA Crypt.

::DEVELOPER

Heider Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 DNA-Crypt

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 May 29;8:176.
DNA-based watermarks using the DNA-Crypt algorithm.
Heider D, Barnekow A.

Phylo 3.3.2 / Open-Phylo – Gaming Framework to Align Genomic Data

Phylo 3.3.2 / Open-Phylo

:: DESCRIPTION

Phylo is a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context.

Open-Phylo is an open crowd-computing platform to solve the multiple sequence alignment problem.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Phylo ; for iSO; for Android

:: MORE INFORMATION

Citation:

Genome Biol. 2013;14(10):R116.
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.
Kwak D, Kam A, Becerra D, Zhou Q, Hops A, Zarour E, Kam A, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.
Phylo: a citizen science approach for improving multiple sequence alignment.
Kawrykow A1, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

Colony B 2.5.1 – mobile Game for analysing Microbiome data

Colony B 2.5.1

:: DESCRIPTION

Colony B is a fast paced puzzle game specifically designed for phones and tablets. In Colony B, you are in charge of growing a colony of bacteria. Bacteria accumulate to survive. Your goal is to identify clusters of bacteria that are accumulating. Theses clusters generate points based on their density, and allow you in turn to grow your colony.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

:: REQUIREMENTS

  • iOS/ Android

:: DOWNLOAD

Colony B for iPhone / for Android phone

:: MORE INFORMATION

Rosetta@home 3.65 – Grid Software for Protein Folding

Rosetta@home 3.65

:: DESCRIPTION

Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s.

::DEVELOPER

The Baker Laboratory , Departments of Computer Science & Engineering and BiochemistryUniversity of Washington

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • BOINC

:: DOWNLOAD

BOINC (enter the project URL: http://boinc.bakerlab.org/rosetta)

:: MORE INFORMATION

Periodic Table 3.2.0 – Desktop Periodic Table.

Periodic Table 3.2.0

:: DESCRIPTION

This interactive Periodic Table (application/applet) has been designed as a learning tool to help the beginning high school or undergraduate chemistry student gain insight. It could be used either as a lecture aid or distributed to students.

::DEVELOPER

Thundercloud Consulting, LLC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX/ Web Browser
  • Java

:: DOWNLOAD

 Periodic Table

:: MORE INFORMATION