COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical... Show moreCOMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data. Show less
Travin, D.; Popov, I.; Guler, A.T.; Medvedev, D.; Plas-Duivesteijn, S. van der; Varela, M.; ... ; Palmblad, M. 2018
Open Science is encouraged by the European Union and many other political and scientific institutions.However, scientific practice is proving slow to change.We propose, as early career researchers,... Show moreOpen Science is encouraged by the European Union and many other political and scientific institutions.However, scientific practice is proving slow to change.We propose, as early career researchers, that it is our task to change scientific research into open scientificresearch and commit to Open Science principles. Show less
Kolder, I.C.R.M.; Plas-Duivesteijn, S.J. van der; Tan, G.; Wiegertjes, G.F.; Forlenza, M.; Guler, A.T.; ... ; Spaink, H.P. 2016
BACKGROUND\nThe common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is... Show moreBACKGROUND\nThe common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.\nRESULTS\nHere we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.\nCONCLUSIONS\nThe identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes. Show less
Guler, A.T.; Waaijer, C.J.F.; Mohammed, Y.; Palmblad, M. 2016
Quantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad... Show moreQuantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad analyses and statistics. The Europe PubMed Central (PMC) and its Web Services is one of these resources, providing a rich platform to retrieve information and metadata on scientific publications. However, a complete bibliometric analysis that involves gathering information and deriving statistics on an author, topic, or country is laborious when consuming Web Services on the command-line or using low level automation. In contrast, scientific workflow managers can integrate different types of software tools to automate multi-step processes. The Taverna workflow engine is a popular open-source scientific workflow manager, giving easy access to availableWeb Services. In this tutorial, we demonstrate how to design scientific workflows for bibliometric analyses in Taverna by integrating Europe PubMed Central Web Services and statistical analysis tools. To our knowledge, this is also the first time scientific workflow managers have been used to perform bibliometric analyses using these Web Services. Show less
Guler, A.T.; Waaijer, C.J.F.; Mohammed, Y.; Palmblad, M. 2016
Quantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad... Show moreQuantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad analyses and statistics. The Europe PubMed Central (PMC) and its Web Services is one of these resources, providing a rich platform to retrieve information and metadata on scientific publications. However, a complete bibliometric analysis that involves gathering information and deriving statistics on an author, topic, or country is laborious when consuming Web Services on the command-line or using low level automation. In contrast, scientific workflow managers can integrate different types of software tools to automate multi-step processes. The Taverna workflow engine is a popular open-source scientific workflow manager, giving easy access to available Web Services. In this tutorial, we demonstrate how to design scientific workflows for bibliometric analyses in Taverna by integrating Europe PubMed Central Web Services and statistical analysis tools. To our knowledge, this is also the first time scientific workflow managers have been used to perform bibliometric analyses using these Web Services. (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Show less
Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They... Show moreScientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics. Show less
Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They... Show moreScientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics. Show less
