Visualize omics data on networks with Omics Visualizer, a Cytoscape App

Cytoscape is an open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources, Cytoscape allows users to import tabular node data and visualize it onto networks. Unfortunately, such data tables can only contain one row of data per node, whereas omics data often have multiple rows for the same gene or protein, representing different post-translational modification sites, peptides, splice isoforms, or conditions. Here, we present a new app, Omics Visualizer, that allows users to import data tables with several rows referring to the same node, connect them to one or more networks, and visualize the connected data onto networks. Omics Visualizer uses the Cytoscape enhancedGraphics app to show the data either in the nodes (pie visualization) or around the nodes (donut visualization), where the colors of the slices represent the imported values. If the user does not provide a network, the app can retrieve one from the STRING database using the Cytoscape stringApp. The Omics Visualizer app is freely available at https://apps.cytoscape.org/apps/omicsvisualizer.

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The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development

Journal of Integrative Bioinformatics ◽

10.1515/jib-2019-0057 ◽

2019 ◽

Vol 16 (3) ◽

Cited By ~ 1

Author(s):

Bjorn Sommer

Keyword(s):

Open Source ◽

Open Source Software ◽

Biological Networks ◽

Special Focus ◽

Database Integration ◽

Software Suite ◽

Software Frameworks ◽

Cell Components ◽

History Of ◽

Student Projects

AbstractFor more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

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MOBN: an interactive database of multi-omics biological networks

10.1101/662502 ◽

2019 ◽

Cited By ~ 1

Author(s):

Cheng Zhang ◽

Muhammad Arif ◽

Xiangyu Li ◽

Sunjae Lee ◽

Abdellah Tebani ◽

...

Keyword(s):

Biological Networks ◽

Gut Microbiome ◽

Clinical Chemistry ◽

Omics Data ◽

Plasma Proteome ◽

Specific Context ◽

Link Type ◽

Single Feature ◽

Plasma Metabolome ◽

Female Specific

AbstractSummaryThe associations among different omics are essential to understand human wellness and disease. However, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present an interactive database of multi-omics biological networks (MOBN) and describe associations between clinical chemistry, anthropometrics, plasma proteome, plasma metabolome and gut microbiome obtained from the same individuals. MOBN allows the user to interactively explore the association of a single feature with other omics data and customize its specific context (e.g. male/female specific). MOBN is designed for users who may not have a formal bioinformatics background to facilitate research in human wellness and diseases.AvailabilityThe database is accessible at http://multiomics.inetmodels.com without any limitation.

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Arteria: An automation system for a sequencing core facility

10.1101/214858 ◽

2017 ◽

Cited By ~ 1

Author(s):

Johan Dahlberg ◽

Johan Hermansson ◽

Steinar Sturlaugsson ◽

Pontus Larsson

Keyword(s):

Conceptual Framework ◽

Open Source ◽

Open Source Software ◽

Modular Design ◽

Automation System ◽

Sequencing Data ◽

Plug And Play ◽

Link Type ◽

Core Facilities ◽

Event Based

AbstractArteria is an automation system aimed at sequencing core facilities. It is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. Herein we describe the Arteria system and elaborate on the underlying conceptual framework. The Arteria system breaks down into three conceptual levels; orchestration, process and execution. At the orchestration level it utilizes an event-based model of automation. It models processes, e.g. the steps involved in processing sequencing data, as workflows and executes these in a micro-service based environment. This creates a system which is both flexible and scalable. The Arteria Project code is available as open source software at http://www.github.com/arteria-project.

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Der Fachinformationsdienst Buch-, Bibliotheks- und Informationswissenschaft – eine Kurzvorstellung

Information - Wissenschaft & Praxis ◽

10.1515/iwp-2019-2062 ◽

2020 ◽

Vol 71 (1) ◽

pp. 43-48

Author(s):

Bettina Gierke

Keyword(s):

Open Source ◽

Open Source Software ◽

Link Type

ZusammenfassungIm Rahmen des DFG Förderprogramms Fachinformationsdienste (FID) nahm der FID Buch- Bibliotheks- und Informationswissenschaft, eine Kooperation der Herzog August Bibliothek Wolfenbüttel und der Universitätsbibliothek Leipzig, im Oktober 2017 seine Arbeit auf. Ziel ist, die Spitzenversorgung mit Literatur für Wissenschaftlerinnen und Wissenschaftler dieser und angrenzenden Disziplinen sicher zu stellen. Dazu hat der FID BBI ein Discovery Tool entwickelt. Grundlage dafür ist die Open-Source-Software VuFind. Eine Herausforderung für den FID BBI ist die Auswertung unterschiedlichster Datenquellen, weil die Themengebiete des FID BBI sehr weit gefächert sind. Das Portal bietet einen schnellen Rechercheeinstieg. Es ist aber auch möglich komplexere Suchanfragen zu stellen. Der Kontakt zu der wissenschaftlichen Gemeinschaft, die der FID BBI bedient, hat große Priorität, um die Ziele, die von der Deutschen Forschungsgemeinschaft gesetzt wurden, zu erfüllen. Ein erster Kontakt kann über das Nachweisportal hergestellt werden: https://katalog.fid-bbi.de.

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CellTool: an open source software combining bio-image analysis and mathematical modeling

10.1101/454256 ◽

2018 ◽

Author(s):

Georgi Danovski ◽

Teodora Dyankova ◽

Stoyno Stoynov

Keyword(s):

Mathematical Modeling ◽

Image Analysis ◽

Open Source ◽

Open Source Software ◽

Time Lapse ◽

Supplementary Information ◽

Data Sets ◽

Link Type ◽

Sample Data ◽

Supplementary Material

AbstractSummaryWe present CellTool, a stand-alone open source software with a Graphical User Interface for image analysis, optimized for measurement of time-lapse microscopy images. It combines data management, image processing, mathematical modeling and graphical presentation of data in a single package. Multiple image filters, segmentation and particle tracking algorithms, combined with direct visualization of the obtained results make CellTool an ideal application for rapid execution of complex tasks. In addition, the software allows for the fitting of the obtained results to predefined or custom mathematical models. Importantly, CellTool provides a platform for easy implementation of custom image analysis packages written on a variety of programing languages.Availability and ImplementationCellTool is a free software available for MS Windows OS under the terms of the GNU General Public License. Executables and source files, supplementary information and sample data sets are freely available for download at URL: https://dnarepair.bas.bg/software/CellTool/[email protected]; [email protected];Supplementary informationSupplementary data are available at URL: https://dnarepair.bas.bg/software/CellTool/Program/CellTool_UserGuide.pdf

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Boiler: Lossy compression of RNA-seq alignments using coverage vectors

10.1101/040634 ◽

2016 ◽

Author(s):

Jacob Pritt ◽

Ben Langmead

Keyword(s):

Open Source ◽

Open Source Software ◽

Negative Impact ◽

Software Tool ◽

Lossy Compression ◽

Rna Seq ◽

Empirical Distributions ◽

Free Open Source Software ◽

Link Type ◽

Free Open Source

AbstractWe describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler.

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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

10.1101/367755 ◽

2018 ◽

Cited By ~ 2

Author(s):

Luis Pedro Coelho ◽

Renato Alves ◽

Paulo Monteiro ◽

Jaime Huerta-Cepas ◽

Ana Teresa Freitas ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Domain Specific Language ◽

Next Generation ◽

Specific Language ◽

Sequence Processing ◽

Domain Specific ◽

Link Type ◽

Fast Processing ◽

User Friendly

AbstractNGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility.Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible. These pipelines can easily be customized and extended with other tools.NGLess and NG-meta-profiler are open source software (under the liberal MIT licence) and can be downloaded from http://ngless.embl.de or installed through bioconda.

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The 2016 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽

10.12688/f1000research.9663.1 ◽

2016 ◽

Vol 5 ◽

pp. 2464

Author(s):

Nomi L. Harris ◽

Peter J.A. Cock ◽

Brad Chapman ◽

Christopher J. Fields ◽

Karsten Hokamp ◽

...

Keyword(s):

Software Development ◽

Open Source ◽

Open Source Software ◽

Open Science ◽

Research Community ◽

Biological Research ◽

Non Profit ◽

Link Type ◽

Bioinformatics Software ◽

Bioinformatics Community

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC (http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

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Exploring biological networks in 3D, stereoscopic 3D and immersive 3D with iCAVE

10.1101/212126 ◽

2017 ◽

Author(s):

Selim Kalaycı ◽

Zeynep H. Gümüş

Keyword(s):

Complex Networks ◽

Open Source ◽

Open Source Software ◽

Biological Networks ◽

Clustering Algorithms ◽

Software Tool ◽

Stereoscopic 3D ◽

Research Fields ◽

Network Layout ◽

3D Network

ABSTRACTBiological networks are becoming increasingly large and complex, pushing the limits of existing 2D tools. iCAVE is an open source software tool for interactive visual explorations of large and complex networks in 3D, stereoscopic 3D or immersive 3D. It introduces new 3D network layout algorithms and 3D-extensions of popular 2D network layout, clustering and edge bundling algorithms to assists researchers in understanding the underlying patterns in large, multi-layered, clustered or complex networks. This protocol aims to guide new users on the basic functions of iCAVE for loading data, laying out networks (single or multi-layered), bundling edges, clustering networks, visualizing clusters, visualizing data attributes and saving output images or videos. It also provides examples on visualizing networks constrained in physical 3D space (e.g. proteins; neurons; brain). It is accompanied with a new version of iCAVE with an enhanced user interface and highlights new features useful for existing users.Significance StatementNetwork representations assist in systems-level data exploration in many research fields, providing valuable insights. However, with the recent advances in experimental technologies, biological networks are becoming increasingly large and complex, necessitating new data visualization solutions. We have recently developed iCAVE (Liluashvili et al., 2017), an open?source software platform that enables 3D (optionally stereoscopic and or immersive) visualizations of complex, dense or multi?layered biological networks. Users can select from several new 3D network layout and clustering algorithms, bundle network edges and customize network attributes to reveal hidden structures within them. This protocol guides new users on loading, navigating, customizing and saving networks in iCAVE and is accompanied by an updated version of the software.

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