From aab2140237f202a9992adf148cb17974c9bfb220 Mon Sep 17 00:00:00 2001 From: Petr Novak Date: Mon, 25 Mar 2024 10:03:51 +0100 Subject: [PATCH] front page updated --- files/galaxy/static/welcome.html | 278 ++++++------------------------- 1 file changed, 52 insertions(+), 226 deletions(-) diff --git a/files/galaxy/static/welcome.html b/files/galaxy/static/welcome.html index 003f1d1..89d5872 100644 --- a/files/galaxy/static/welcome.html +++ b/files/galaxy/static/welcome.html @@ -1,12 +1,4 @@ - - - - - - RepeatExplorer server - - - - - - - - Welcome to RepeatExplorer - - -

Developed and maintained by the Laboratory - of Molecular Cytogenetics, Institute of Plant Molecular Biology, - Biology Centre CAS, Ceske Budejovice, Czech Republic

-

This RepeatExplorer Galaxy portal is a part of services provided - by ELIXIR - (European research infrastructure for biological information). Please - acknowledge this fact in your publications by adding a statement: - “Computational - resources for RepeatExplorer analysis were provided by the ELIXIR-CZ - project (LM2023055), part of the international ELIXIR - infrastructure.” -

- -
- - - ELIXIR - -
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Resources

- - - Follow @RepeatExplorer - - -
- -

Updates

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Oct 23, 2020

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Step by step protocols were published in - Nature Protocols

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Jan 13, 2020

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Galaxy server was updated to version 19.09

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Jan 13, 2020

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RepeatExplorer2 and TAREAN tools were updated - to version 2.3.7

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See changelog for detailed description of included changes. - Previous versions can be found in Obsolete tools section -

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Jan 8, 2020

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RepeatExplorer tools are now available in - Galaxy toolshed

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Packages repeatexplorer2, dante and re_utils can be installed - from Galaxy toolshed to custom Galaxy instance if you prefer - analysis using RepeatExplorer on on your server.

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Nov 10, 2019

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Data quota increased to 200G

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Data quota for registered users was increased from 50G to 200G - to enable easier analysis of larger datasets

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Changelog -

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Information about changes in - RepeatExplorer programs can be found in its repository changelog. -

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Contact information

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If you need a help or you want to - report a problem, please contact server - administrator. -

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How to Cite

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Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

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Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - - RepeatExplorer: - a Galaxy-based web server for genome-wide characterization of - eukaryotic repetitive elements from next generation sequence reads. - Bioinformatics 29:792-793. -

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Classification of repetitive elements using REXdb:

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Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – - Systematic - survey of plant LTR-retrotransposons elucidates phylogenetic - relationships of their polyprotein domains and provides a reference - for element classification. Mobile DNA 10:1.

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The principle of repeat identification implemented in the - RepeatExplorer: -

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Novak, P., Neumann, P., Macas, J. (2010) - Graph-based - clustering and characterization of repetitive sequences in - next-generation sequencing data. BMC Bioinformatics - 11:378. -

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Using TAREAN for satellite repeat detection and - characterization: -

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Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, - P., Macas, J. (2017) - TAREAN: - a computational tool for identification and characterization of - satellite DNA from unassembled short reads. Nucleic Acid - Research 45:e111 -

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- -
- - - ELIXIR - -
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Terms of Use -

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RepeatExplorer is provided as free, public, Internet accessible - service, in the hope that it will be useful, but WITHOUT ANY - WARRANTY. Data transfer are encrypted, but data storage are not. If - there are restrictions on the way your research data can be stored - and used, please consult your local institutional review board or the - project PI before uploading it to this Galaxy server. If you have - protected data, large data storage requirements, or short deadlines - you are encouraged to setup your own local Galaxy instance with - RepeatExplorer Alternatively, you can install only RepeatExplorer and - use its command line version. If you need help with - RepeatExplorer or you want to report a problem, please contact server - administrator -

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- -

- - + + +

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Developed and maintained by the Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic

+

This RepeatExplorer Galaxy portal is a part of services provided by ELIXIR (European Research Infrastructure for Biological Information). Please acknowledge this fact in your publications by adding a statement: “Computational resources for RepeatExplorer analysis were provided by the ELIXIR-CZ project (LM2023055), part of the international ELIXIR infrastructure.”

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+

ELIXIR

+
+
+

Contact information

+

If you need help, need to increase a data quota, or want to report a problem, please contact server administrator. If you encounter an error while running a tool, please report a bug using the bug icon in the dataset history.

+
+

Resources

+ +Follow @RepeatExplorer + +
+

Common Use Cases of RepeatExplorer Server

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The RepeatExplorer server provides a suite of tools designed for the comprehensive analysis of repetitive DNA sequences in genomic data. Here are the most common use cases for utilizing these tools:

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+

How to Cite

+

Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

+

Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793.

+

Classification of repetitive elements using REXdb:

+

Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.

+

The principle of repeat identification implemented in the RepeatExplorer:

+

Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.

+

Using TAREAN for satellite repeat detection and characterization:

+

Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research 45:e111

+
+

Terms of Use

+

RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer are encrypted, but data storage is not. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to set up your own local Galaxy instance with RepeatExplorer Alternatively, you can install only RepeatExplorer and use its command line version. If you need help with RepeatExplorer or you want to report a problem, please contact server administrator.

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