Path2Models – Collection of Models automatically generated from Pathway Resources

Path2Models

:: DESCRIPTION

Path2Models automatically generates mathematical models from biological pathway representations using a suite of freely available software. Computed models from over 2600 organisms encoded in SBML and SBGN are available through the BioModels Database.

::DEVELOPER

BioModels team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, et al.
BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

TrackSM 1.00 – Associate Chemical Compound to Known Metabolic Pathway

TrackSM 1.00

:: DESCRIPTION

TrackSM is a cheminformatics tool which designs to associate a chemical compound to a known metabolic pathway based on molecular structure matching techniques.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

 TrackSM

:: MORE INFORMATION

Citation

J Chem Inf Model. 2015 Mar 23;55(3):709-18. doi: 10.1021/ci500517v.
Metabolic pathway predictions for metabolomics: a molecular structure matching approach.
Hamdalla MA1, Rajasekaran S, Grant DF, Măndoiu II.

Epi-Seq 1.0.0 – Predicting Tumor Specific Epitopes from RNA-Seq data

Epi-Seq 1.0.0

:: DESCRIPTION

Epi-Seq is a multi-step bioinformatics analysis pipeline that starts from the raw RNA-Seq tumor reads, and produces a set of predicted tumor-specific expressed epitopes.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Epi-Seq

:: MORE INFORMATION

SILP2 – ILP-based Maximum Likelihood Genome Scaffolding

SILP2

:: DESCRIPTION

SILP2 is a stand-alone scaffolding tool that generates maximum likelihood scaffolds via integer linear programming (ILP). SILP2 achieves high scalability without sacrificing optimality by solving the large ILP formulations required to scaffold mammalian-size genomes via a non-serial dynamic programming (NSDP) approach based on decomposing the scaffolding graph into 3-connected components.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SILP2

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.
ILP-based maximum likelihood genome scaffolding.
Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

SC1 – A web-based Single Cell RNA-seq Analysis Pipeline

SC1

:: DESCRIPTION

SC1 is a web-based single cell RNA-seq analysis pipeline.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

J Comput Biol. 2019 Aug;26(8):822-835. doi: 10.1089/cmb.2018.0236. Epub 2019 Feb 19.
Locality Sensitive Imputation for Single Cell RNA-Seq Data.
Moussa M, Măndoiu II.

TCLP – Online Cancer Cell Line Catalogue integrating HLA type

TCLP

:: DESCRIPTION

TCLP (TRON CELL LINE PORTAL)is the largest catalog of cancer cell line annotations integrating HLA type, HLA expression, predicted HLA Class I and Class II neo-epitopes, virus, and gene expression.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Scholtalbers J, Boegel S, Bukur T, Byl M, Goerges S, Sorn P, Loewer M, Sahin U, Castle JC:
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome medicine 2015, 7:118.

ArtiFuse v1.0.0 – Computational Validation of Fusion Gene Detection tools without relying on simulated reads

ArtiFuse v1.0.0

:: DESCRIPTION

ArtiFusion is a tool to simulate artificial fusion events by modifying a given reference genome. The tool copies parts of the exonic sequence of gene A within the reference genome FASTA sequence into the downstream region of gene B and replaces the copied regions of gene A with Ns. The breakpoints are defined by using a size ratio between gene A and gene B and are always placed on exon-exon junctions. Intronic and intergenic regions remain unchanged.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

ArtiFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz613. doi: 10.1093/bioinformatics/btz613.
ArtiFuse – Computational validation of fusion gene detection tools without relying on simulated reads.
Sorn P, Hohlsträter C, Löwer M, Sahin U, Weber D.

Galaxy LIMS – LIMS for Next-generation Sequencing

Galaxy LIMS

:: DESCRIPTION

Galaxy LIMS is a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Galaxy LIMS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1233-4. doi: 10.1093/bioinformatics/btt115. Epub 2013 Mar 11.
Galaxy LIMS for next-generation sequencing.
Scholtalbers J, Rößler J, Sorn P, de Graaf J, Boisguérin V, Castle J, Sahin U.

GEMINI – The Genomic Search Engine

GEMINI

:: DESCRIPTION

GEMINI is an open-source bioinformatics tool and website written in python to facilitate near-neighbor searching of genomic data.

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GEMINI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Feb 24;17:102. doi: 10.1186/s12859-016-0934-8.
GEMINI: a computationally-efficient search engine for large gene expression datasets.
DeFreitas T, Saddiki H, Flaherty P

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)