scds 1.2.0 – In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

scds 1.2.0

:: DESCRIPTION

scds (single cell doublet scoring) is a software of computational doublet prediction for single cell RNA sequencing data

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • BioConductor

:: DOWNLOAD

scds

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Sep 10. pii: btz698. doi: 10.1093/bioinformatics/btz698.
scds: Computational Annotation of Doublets in Single-Cell RNA Sequencing Data.
Bais AS, Kostka D.

LongISLND 0.9.5 – In silico Sequencing of Lengthy and Noisy Datatypes

LongISLND 0.9.5

:: DESCRIPTION

LongISLND is a read simulator which profiles the characteristics of third generation, single-molecule sequencing technologies and simulates accordingly.

::DEVELOPER

Roche Sequencing Solutions

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Python
  • Java
  • Maven

:: DOWNLOAD

LongISLND

:: MORE INFORMATION

Citation

LongISLND: in silico sequencing of lengthy and noisy datatypes.
Lau B, Mohiyuddin M, Mu JC, Fang LT, Bani Asadi N, Dallett C, Lam HY.
Bioinformatics. 2016 Dec 15;32(24):3829-3832. Epub 2016 Sep 25.

AMMOS / DG-AMMOS – Automated Molecular Mechanics Optimization tool for in silico Screening / using Distance Geometry

AMMOS / DG-AMMOS

:: DESCRIPTION

AMMOS is a package to refine the 3D structures of compounds and of compounds docked into a protein target.

DG-AMMOS is a New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening.

::DEVELOPER

Molécules Thérapeutiques in silico (MTi)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 AMMOS / DG-AMMOS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Oct 16;9:438. doi: 10.1186/1471-2105-9-438.
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA.

BMC Chem Biol. 2009 Nov 13;9:6. doi: 10.1186/1472-6769-9-6.
DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.
Lagorce D, Pencheva T, Villoutreix BO, Miteva MA.

MetISIS 1.0 – Metabolite In Silico Identification Software

MetISIS 1.0

:: DESCRIPTION

MetISIS (Metabolite In Silico Identification Software) is a software application that takes user observed MS/MS spectra and generates ranked lists of candidate identifications from a database of metabolites.

::DEVELOPER

Lars Kangas (Lars.Kangas@pnnl.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 2.0

:: DOWNLOAD

 MetISIS

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1705-13. doi: 10.1093/bioinformatics/bts194. Epub 2012 May 15.
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.
Kangas LJ1, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH.

FindPath – in silico Design of Synthetic Metabolic Pathways

FindPath

:: DESCRIPTION

FindPath is an unified system predicting and ranking the possible pathways according to their metabolic efficiency in cellular context. This tool rely on chemical reactions database to generate all possible metabolic pathways and exploits constraint-based models (CBMs) to identify the synthetic pathway that is the most effective for achieving a desired metabolic function in a given host microorganism.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • MatLab

:: DOWNLOAD

 FindPath

:: MORE INFORMATION

Citation

FindPath: A Matlab solution for in silico design of synthetic metabolic pathways.
Gilles V, Marc C, Jean-Charles P, Stéphanie H.
Bioinformatics. 2014 Jul 3. pii: btu422.

ISIF 1.1.3 – Performs in silico AFLP

ISIF 1.1.3

:: DESCRIPTION

ISIF (In SIlico Fingerprinting) is a free user-friendly software that performs in silico AFLP (can also be applied for DART or RAD).

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

ISIF

:: REQUIREMENTS

  • Windows with .net 2.0 

:: DOWNLOAD

 ISIF

:: MORE INFORMATION

Citation

Paris, M., Bonnes, B., Ficetola, G.F., Poncet, B.N., Despres, L. (2010)
Amplified fragment length homoplasy: in silico analysis for model and non-model species.
BMC Genomics 11:287.

GEPIS – Gene Expression Profiling in silico

GEPIS

:: DESCRIPTION

GEPIS (Gene Expression Profiling in silico), is a bioinformatics tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples.

::DEVELOPER

UCSF CGL -Genentech Collaboration

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood and Zemin Zhang
GEPIS-quantitative gene expression profiling in normal and cancer tissues
Bioinformatics, Oct. 12 2004, Vol. 20, No. 15, pp2390-2398

IBRENA 1.0 – In silico Biochemical Reaction Network Analysis

IBRENA 1.0

:: DESCRIPTION

IBRENA (Insilico Biochemical REaction Network Analysis) is a software to aid the analysis of complex biological reaction networks. In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis.

::DEVELOPER

Sriram Neelamegham 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 IBRENA

:: MORE INFORMATION

Citation

Liu, G. and S. Neelamegham,
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks.
Bioinformatics (2008) 24 (8): 1109-1111.

 

ISS – In-silico Gene Sequencing Method

ISS

:: DESCRIPTION

ISS (in silico gene sequencing method) predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of the method is to infer diploid sequences (a pair of phased sequences/alleles) at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ISS

:: MORE INFORMATION

Citation

Zhang XC, Zhang B, Li SS, Huang X, Hansen JA, Zhao LP
Sequencing Genes in-silico Using Single Nucleotide Polymorphisms.
BMC Genetics 2012, 13:6