New tools or new releases with additional features arrive at an enormous pace, and new reference data or concepts for quality control are emerging. Workflows in data-driven science such as computational biology have considerably gained in complexity. However, for most academic environments with local expertise, novel data collection techniques or novel data analysis, it is essential to have all the flexibility of open-source tools and open-source workflow descriptions. Commercial providers tend to offer prepared applications remote to their clients. A range of popular workflow suites are available to support analyses in computational biology.
Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics.
Icsviewer wiki pdf#
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from citations in the text to the list of References) and hyperlinks (e.g. In the electronic version (in PDF), the main thesis is optimised for reading on a screen, with clickable cross-references (e.g. In the printed version, the three articles that are part of this thesis, are attached after the Discussion and References. The Discussion chapter presents further considerations and current work, and concludes the discussed contributions with alternative and future perspectives. Summary of results summarises the contributions of my enclosed projects – the BioXSD data format, the EDAM ontology, and the eSysbio workbench prototype – to the broad topics of the thesis. The thesis is organised as follows: In the Background chapter, the field is presented, with various approaches and existing efforts. I also mention some closely related efforts that I have been involved in.
Icsviewer wiki software#
In addition to these three main contributions that I have been involved in, I present a comprehensive but non-exhaustive research into the various previous and contemporary efforts and approaches to the broad topic of integrative bioinformatics, in particular with respect to bioinformatics software and services. We aimed at utilising the World-Wide-Web and industrial standards, in order to increase compatibility and maintainability, and foster shared effort. The eSysbio project explored ways of developing a workbench for collaborative data analysis, accessible in various ways for users with various tasks and expertise. EDAM can be helpful in documenting and categorising bioinformatics resources using a standard “vocabulary”, enabling users to find respective resources and choose the right tools. The EDAM ontology aimed at enumerating and organising concepts within bioinformatics, including operations and types of data. In the BioXSD project, we aimed at developing an XML-Schema-based data format compatible with Web services and programmatic libraries, that is expressive enough to be usable as a common, canonical data model that serves tools, libraries, and users with convenient data interoperability. As diverse components are necessary for the accessible and reliable bioinformatics scenario, our work focussed in particular on the following: Many approaches are possible and necessary towards these goals, and many layers need to be tackled, in collaborative community efforts with well-defined scope. Information about the version of each plugin:ĩf4f8151 (OBSOLETE_UNINSTALLED) 20140707074617 jars/jython-2.5.2.The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Information relevant to JAVA_HOME related problems: Java.vm.name => Java HotSpot(TM) 64-Bit Server VM ids type of files, hoping we can still do that. I've heard that Image J used to be able to open the. : ICS file not found.Īt .ICSReader.initFile(ICSReader.java:775)Īt (FormatReader.java:1317)Īt .ImportProcess.initializeFile(ImportProcess.java:494)Īt .ImportProcess.execute(ImportProcess.java:144)Īt .Importer.showDialogs(Importer.java:141)Īt .n(Importer.java:79)Īt (LociImporter.java:81)Īt ij.nCommand(Executer.java:131) But then it says, "Sorry, there was a problem during import" and the text window (log) that pops up says this: ids file here to open, and at first it looks like this is going fine.
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