Panache v1.0.0 – PANgenome Analyzer with CHromosomal Exploration

Panache v1.0.0

:: DESCRIPTION

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

::DEVELOPER

Panache team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Durant É, Sabot F, Conte M, Rouard M.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes.
Bioinformatics. 2021 Oct 2:btab688. doi: 10.1093/bioinformatics/btab688. Epub ahead of print. PMID: 34601567.

iDNA-ABT – Detecting DNA Methylation with Adaptive Features and Transductive Information Maximization

iDNA-ABT

:: DESCRIPTION

iDNA-ABT is an advanced deep learning model that utilizes adaptive embedding based on bidirectional transformers for language understanding (BERT) together with a novel transductive information maximization (TIM) loss.

::DEVELOPER

iDNA-ABT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

iDNA-ABT

:: MORE INFORMATION

Citation

Yu Y, He W, Jin J, Cui L, Zeng R, Wei L.
iDNA-ABT : advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.
Bioinformatics. 2021 Oct 2:btab677. doi: 10.1093/bioinformatics/btab677. Epub ahead of print. PMID: 34601568.

JChem for Office 21.15.603 – Chemical Structure Handling & Visualizing within Microsoft Office

JChem for Office 21.15.603

:: DESCRIPTION

JChem for Office integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails. Implementation is robust with fast loading/scrolling of many thousands of structure rows and copy-paste throughout the Microsoft Office suite. More advanced functionality includes: structure based calculations, R-group decomposition and library enumeration.

::DEVELOPER

ChemAxon Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Microsoft Office®

:: DOWNLOAD

 JChem for Office

:: MORE INFORMATION

TopPIC 1.6 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

TopPIC 1.6

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

TopPIC team

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.

CSS-Palm 4.0 – Palmitoylation Site Prediction with a Clustering and Scoring Strategy

CSS-Palm 4.0

:: DESCRIPTION

CSS-Palm is a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction.The program’s prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6).

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 CSS-Palm

:: MORE INFORMATION

Citation

CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Jian Ren, Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao.
Protein Engineering, Design and Selection.2008 21(11):639-644

QGAStation 2.0 – Software for the Classical Quantitative Genetics

QGAStation 2.0

:: DESCRIPTION

QGAStation has several features: Handle complicated genetic models for agronomic traits, seed traits, and developmental traits; Analyze unbalanced data; Combine jackknifing techniques to test the significance of each genetic parameter; Some important references are listed in the result files.

::DEVELOPER

ZJU-IBI

:: SCREENSHOTS

:: REQUIREMENTS

  • windows/MacOsX

:: DOWNLOAD

 QGAStation

:: MORE INFORMATION

CFC 1.0 – Monitor Genetic Diversity

CFC 1.0

:: DESCRIPTION

CFC is originally developed to compute population statistics on relationships by a computationally efficient indirect method.

::DEVELOPER

Mehdi Sargolzaei

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CFC

:: MORE INFORMATION

Citation

Sargolzaei, M., H. Iwaisaki and J.J. Colleau. 2006.
CFC: A tool for monitoring genetic diversity.
Proc. 8th World Congr. Genet. Appl. Livest. Prod., CD-ROM Communication 27-28. Belo Horizonte, Brazil, Aug. 13-18, 2006.

Network 10.2.0.0 – Phylogenetic Network Software

Network 10.2.0.0

:: DESCRIPTION

Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.

::DEVELOPER

Fluxus Technology Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Network

:: MORE INFORMATION

Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

RocketBugs / RocketBugsRender – Simulation of the Actin-based Motility of Listeria Monocytogenes

RocketBugs / RocketBugsRender

:: DESCRIPTION

RocketBugs is a simulation of the actin-based motility of Listeria monocytogenes.

RocketBugsRender is a special rendering and graphing program for the simulation output of “RocketBugs”, the actin-based Listeria motility simulations

::DEVELOPER

The Center for Cell Dynamics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

RocketBugs  ,RocketBugsRender

:: MORE INFORMATION

Citation

Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell
An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
PLoS Comput Biol 5(7): e1000434. doi:10.1371/journal.pcbi.1000434