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López-Fernández H, Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research. Comput Biol Med 2019; 107:197-205. [PMID: 30849608 DOI: 10.1016/j.compbiomed.2019.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 01/31/2023]
Abstract
BACKGROUND Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but available analysis tools are often hard to install, configure and use by users without advanced bioinformatics skills. METHODS Within reason, DEWE aims to make RNA-Seq analysis as easy for non-proficient users as for experienced bioinformaticians. DEWE supports two well-established and widely used differential expression analysis workflows: using Bowtie2 or HISAT2 for sequence alignment; and, both applying StringTie for quantification, and Ballgown and edgeR for differential expression analysis. Also, it enables the tailored execution of individual tools as well as helps with the management and visualisation of differential expression results. RESULTS DEWE provides a user-friendly interface designed to reduce the learning curve of less knowledgeable users while enabling analysis customisation and software extension by advanced users. Docker technology helps overcome installation and configuration hurdles. In addition, DEWE produces high quality and publication-ready outputs in the form of tab-delimited files and figures, as well as helps researchers with further analyses, such as pathway enrichment analysis. CONCLUSIONS The abilities of DEWE are exemplified here by practical application to a comparative analysis of monocytes and monocyte-derived dendritic cells, a study of clinical relevance. DEWE installers and documentation are freely available at https://www.sing-group.org/dewe.
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Affiliation(s)
- Hugo López-Fernández
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain; Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Rúa Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Aitor Blanco-Míguez
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Florentino Fdez-Riverola
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Anália Lourenço
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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López-Fernández H, Reboiro-Jato M, Glez-Peña D, Laza R, Pavón R, Fdez-Riverola F. GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components. PLoS One 2018; 13:e0204474. [PMID: 30235322 PMCID: PMC6147514 DOI: 10.1371/journal.pone.0204474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/07/2018] [Indexed: 01/22/2023] Open
Abstract
Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s.
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Affiliation(s)
- Hugo López-Fernández
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
| | - Miguel Reboiro-Jato
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Daniel Glez-Peña
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Rosalía Laza
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Reyes Pavón
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Florentino Fdez-Riverola
- ESEI—Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain
- CINBIO—Centro de Investigaciones Biomédicas, Universidad de Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
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López-Fernández H, Araújo JE, Jorge S, Glez-Peña D, Reboiro-Jato M, Santos HM, Fdez-Riverola F, Capelo JL. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2018; 155:1-9. [PMID: 29512488 DOI: 10.1016/j.cmpb.2017.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND OBJECTIVE 2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. METHODS S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. RESULTS S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. CONCLUSIONS S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis.
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Affiliation(s)
- Hugo López-Fernández
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal.
| | - José E Araújo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Susana Jorge
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Daniel Glez-Peña
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Hugo M Santos
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - José L Capelo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
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Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis. Methods Mol Biol 2018; 1558:437-458. [PMID: 28150251 DOI: 10.1007/978-1-4939-6783-4_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Cell signaling and functions heavily rely on post-translational modifications (PTMs) of proteins. Their high-throughput characterization is thus of utmost interest for multiple biological and medical investigations. In combination with efficient enrichment methods, peptide mass spectrometry analysis allows the quantitative comparison of thousands of modified peptides over different conditions. However, the large and complex datasets produced pose multiple data interpretation challenges, ranging from spectral interpretation to statistical and multivariate analyses. Here, we present a typical workflow to interpret such data.
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Beck F, Weiskopf D. Word-Sized Graphics for Scientific Texts. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2017; 23:1576-1587. [PMID: 28252406 DOI: 10.1109/tvcg.2017.2674958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Generating visualizations at the size of a word creates dense information representations often called sparklines. The integration of word-sized graphics into text could avoid additional cognitive load caused by splitting the readers' attention between figures and text. In scientific publications, these graphics make statements easier to understand and verify because additional quantitative information is available where needed. In this work, we perform a literature review to find out how researchers have already applied such word-sized representations. Illustrating the versatility of the approach, we leverage these representations for reporting empirical and bibliographic data in three application examples. For interactive Web-based publications, we explore levels of interactivity and discuss interaction patterns to link visualization and text. We finally call the visualization community to be a pioneer in exploring new visualization-enriched and interactive publication formats.
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Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehtevä M, Reichl U, Martens L, Rapp E. The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation. J Proteome Res 2015; 14:1557-65. [DOI: 10.1021/pr501246w] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Thilo Muth
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Alexander Behne
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Robert Heyer
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Fabian Kohrs
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Miro Lehtevä
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Udo Reichl
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Erdmann Rapp
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
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