Tag: Function

DCell 1.4 – Deep Neural Network simulating Cell Structure and Function

DCell 1.4

:: DESCRIPTION

DCell is a neural network model of budding yeast, a basic eukaryotic cell. The model structure corresponds exactly to a hierarchy of 2,526 cellular subsystems.

::DEVELOPER

Ma Laboratory / Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DCell

:: MORE INFORMATION

Citation:

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T.
Using deep learning to model the hierarchical structure and function of a cell.
Nat Methods. 2018 Apr;15(4):290-298. doi: 10.1038/nmeth.4627. Epub 2018 Mar 5. PMID: 29505029; PMCID: PMC5882547.

CRISPR-SURF 1.0 – Screening of Uncharacterized Region Function

CRISPR-SURF 1.0

:: DESCRIPTION

CRISPR-SURF is an exploratory and interactive computational framework for the design and analysis of CRISPR-Cas, CRISPRi, and CRISPRa tiling screens.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

CRISPR-SURF

:: MORE INFORMATION

Citation

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L.
CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.
Nat Methods. 2018 Dec;15(12):992-993. doi: 10.1038/s41592-018-0225-6. PMID: 30504875; PMCID: PMC6620603.

OncodriveROLE – Classifying cancer driver genes into Loss of Function and Activating roles.

OncodriveROLE

:: DESCRIPTION

OncodriveROLE is a machine-learning based approach to classify cancer driver genes into to Activating or Loss of Function roles for cancer gene development.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

OncodriveROLE

:: MORE INFORMATION

Citation

Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N.
OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action.
Bioinformatics. 2014 Sep 1;30(17):i549-55. doi: 10.1093/bioinformatics/btu467. PMID: 25161246; PMCID: PMC4147920.

Syntenator 2 – Multiple Gene Order Alignments with a Gene-specific Scoring Function

Syntenator 2

:: DESCRIPTION

Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.

::DEVELOPER

BIMSB Bioinformatics Core.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 Syntenator

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2008 Nov 6;3:14.
Syntenator: multiple gene order alignments with a gene-specific scoring function.
Rödelsperger  C, Dieterich C.

ScienceMatrix – Cell Structure and Function

ScienceMatrix

:: DESCRIPTION

ScienceMatrix: Cell Structure & Function is closely aligned with and supports the middle- and secondary-level science curriculum you are already working with. Taking full advantage of current technology to help you teach science better, it works in conjunction with your existing teaching implements to provide hands-on activities to help students understand even the most challenging topics.

::DEVELOPER

Digital Frog International

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

ScienceMatrix

:: MORE INFORMATION

FindEM 2.0 – Fast Local Correlation Function Particle Picker

FindEM 2.0

:: DESCRIPTION

The FindEM program is based on projection matching using local real-space correlation with a series of templates. Real-space algorithms are traditionally relatively slow, but a fast Fourier based implementation of the real-space local correlation function has been introduced which is approximately two orders of magnitude faster for the projection matching application.

::DEVELOPER

NRAMM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Fortron

:: DOWNLOAD

FindEM

:: MORE INFORMATION

Citation:

J Struct Biol. 2004 Jan-Feb;145(1-2):91-9.
FindEM–a fast, efficient program for automatic selection of particles from electron micrographs.
Roseman AM.

FuncAssociate 2.0 – Gene Sets Characterizing & Functional Trend Analysis

FuncAssociate 2.0

:: DESCRIPTION

FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. FuncAssociate takes a list of genes as input and produces a ranked list of the Gene Ontology terms enriched in an input list.

::DEVELOPER

Roth Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python/Perl

:: DOWNLOAD

 FuncAssociate

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 15;25(22):3043-4. doi: 10.1093/bioinformatics/btp498. Epub 2009 Aug 28.
Next generation software for functional trend analysis.
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP.

ReadqPCR / NormqPCR 1.38.0 / – Read qPCR data / Functions for Normalisation of RT-qPCR data

ReadqPCR / NormqPCR 1.38.0

:: DESCRIPTION

ReadqPCR and NormqPCR are R/Bioconductor packages to analyse RT-qPCR data.

::DEVELOPER

James Perkins <j.perkins at ucl.ac.uk>, Matthias Kohl, Nor Izayu Abdul Rahman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 ReadqPCR and NormqPCR

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 2;13:296. doi: 10.1186/1471-2164-13-296.
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
Perkins JR1, Dawes JM, McMahon SB, Bennett DL, Orengo C, Kohl M.

sydSeq 1.1.7 – Various Functions for Gene Expression Analysis

sydSeq 1.1.7

:: DESCRIPTION

sydSeq is an R package containing the functions exClust, TshrinkPlus and pMim.

::DEVELOPER

Ellis Patrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R

:: DOWNLOAD

 sydSeq

:: MORE INFORMATION

Citation

Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data.
Patrick E, Buckley M, Müller S, Lin DM, Yang JY.
Bioinformatics. 2015 Sep 1;31(17):2822-8. doi: 10.1093/bioinformatics/btv220.

Estimation of data-specific constitutive exons with RNA-Seq data.
Patrick E, Buckley M, Yang YH.
BMC Bioinformatics. 2013 Jan 29;14:31

ENCoM – Exploring Protein Conformational Space and Effect of Mutations on Protein Function and Stability

ENCoM

:: DESCRIPTION

ENCoM is a coarse grained normal modes analysis method to evaluate thermostability of proteins.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ENCoM

:: MORE INFORMATION

Citation

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.
Frappier V, Chartier M, Najmanovich RJ.
Nucleic Acids Res. 2015 Apr 16. pii: gkv343.