cube.univie.ac.at

Computational Systems Biology, University of Vienna

Dept of Microbiology and Ecosystem Science. Bachelor and master projects. Our aim is to advance our understanding of biological systems,. Ranging from single species to multi-species systems and ecosystems,. Based on data from large-scale bioanalytical methods. We develop, improve and apply. For the interpretation of molecular information in biology. We establish and analyse. CUBE and friends BBQ on July 2. New webdesign for CUBE. The CUBE website has been redesigned based on a layout by pion. The Intrap...

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Computational Systems Biology, University of Vienna | cube.univie.ac.at Reviews

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Dept of Microbiology and Ecosystem Science. Bachelor and master projects. Our aim is to advance our understanding of biological systems,. Ranging from single species to multi-species systems and ecosystems,. Based on data from large-scale bioanalytical methods. We develop, improve and apply. For the interpretation of molecular information in biology. We establish and analyse. CUBE and friends BBQ on July 2. New webdesign for CUBE. The CUBE website has been redesigned based on a layout by pion. The Intrap...

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Computational Systems Biology, University of Vienna | cube.univie.ac.at Reviews

https://cube.univie.ac.at

Dept of Microbiology and Ecosystem Science. Bachelor and master projects. Our aim is to advance our understanding of biological systems,. Ranging from single species to multi-species systems and ecosystems,. Based on data from large-scale bioanalytical methods. We develop, improve and apply. For the interpretation of molecular information in biology. We establish and analyse. CUBE and friends BBQ on July 2. New webdesign for CUBE. The CUBE website has been redesigned based on a layout by pion. The Intrap...

INTERNAL PAGES

cube.univie.ac.at

1

CUBE & friends BBQ on July 2 | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/news/cube-friends-bbq-on-july-2

Bachelor and master projects. CUBE and friends BBQ on July 2. We celebrate 5 years of CUBE and invite all recent and former CUBE members and our friends to a BBQ party on Thursday July 2nd. The party will start around 5pm on our terrace. NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.

2

Master studies | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/master-studies

Bachelor and master projects. CUBE contributes to multiple master programs in biology and computational science. We are engaged in designing the upcoming Master Bioinformatics at our university. We recommend the master programs "Computational Science" and "Microbial Ecology" particularly for students who are interested in doing their master thesis at CUBE. The master program in bioinformatics is open to students having a bachelor degree in life science, mathematics or computer science. Master program Mol...

3

Staff | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/people

Bachelor and master projects. Category (field tr staff category). Prof Dr. Thomas Rattei. Head of the Division of Computational Systems Biology. Vice-head of the Department of Microbiology and Ecosystem Science. 43 1 4277 76680. Thomas.rattei@univie.ac.at. 43 1 4277 76682. Florian.goldenberg@univie.ac.at. 43 1 4277 76681. Gabriele.kaindl@univie.ac.at. Thomas.nussbaumer@univie.ac.at. Dr Ing. Alexander Platzer. Alexander.platzer@univie.ac.at. Contact.cube@univie.ac.at. Contact.cube@univie.ac.at. Deep metag...

4

News | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/news

Bachelor and master projects. Job opening: Group Leader Position. The Division of Computational Systems Biology at the University of Vienna is offering a. Group Leader Position in Bioinformatics. CUBE - the division of Computational Systems Biology. Is part of the Department of Microbiology and Ecosystem Science of the . Virus Orthologous Groups: A novel resource for virus (meta)genomics. Normalization visualization tool (NVT) released. Public release of CONSPRED genome annotation pipeline. CONSPRED is a...

5

Similarity Matrix of Proteins (SIMAP) | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/resources/simap

Bachelor and master projects. Similarity Matrix of Proteins (SIMAP). SIMAP - The similarity matrix of proteins. The similarity matrix of proteins is a database of protein sequences, their all-against-all sequence similarities and functional annotations. The database is currently re-implemented, based on a different algorithm for sequence similarity calculation. SIMAP 1 refers to the traditional database, run from 2004 until 2014. SIMAP 2 is the new SIMAP database which has started in 2015. The new SIMAP ...

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effectivedb.org

Documentation and support | EffectiveDB

http://www.effectivedb.org/help

Dept of Microbiology and Ecosystem Science. Job submission to EffectiveDB. Interpretation of EffectiveDB predictions. Frequently asked questions (FAQ). Q: Why the results with different arguments varies considerably, especially when I add EffectiveS346 arguments? Q: Can I run all these tools you used for the database also locally on new sequences/genomes? A: Yes, our computer cluster would be pleased! Q: What does this 'N.D.' mean, which I see sometimes at 'Gram negative:' and following lines? Prediction...

effectivedb.org

Download | EffectiveDB

http://www.effectivedb.org/download

Dept of Microbiology and Ecosystem Science. Precalculations for bacterial genomes. Browsable folder of results for all bacterial genomes from EggNOG 4.0 and selected additional genomes from NCBI RefSeq by NCBI taxonomy ID. ZIP archive of results for all bacterial EggNOG 4.0 genomes by NCBI taxonomy ID. Tab separated values file listing taxonomyids, names and predicted seretion systems for all bacterial EggNOG 4.0 genomes. Current and previous EffectiveELD. Browsable folder of EffectiveELD releases.

effectivedb.org

Effective job submission | EffectiveDB

http://www.effectivedb.org/effective/submit

Dept of Microbiology and Ecosystem Science. Prediction of secreted proteins and protein secretion systems. Main input for your job. Will only be used for job notification and is not stored on the server. One or multiple protein sequences in FASTA format:. FASTA formatted protein sequences. Upload a FASTA formatted protein sequence file. Predicts Type III secreted proteins based on their signal peptide. Select the version of the EffectiveT3. Predicts secreted proteins based on eukaryotic-like domains.

effectivedb.org

New EffectiveDB website | EffectiveDB

http://www.effectivedb.org/news/new-effectivedb-website

Dept of Microbiology and Ecosystem Science. EffectiveDB is now hosted in a new website. It is based on the Drupal. Framework and gives user-friendly access to the contents of the Effective database, allows the submission of compute jobs and provides documentation and supplementary data for specific methods of EffectiveDB. The EffectiveDB team appreciates your feedback on the new website. Prediction of microbial phenotypes based on comparative genomics. 43 1 4277 76681. 43 1 4277 876681.

effectivedb.org

Links | EffectiveDB

http://www.effectivedb.org/links

Dept of Microbiology and Ecosystem Science. Prediction of Type III secreted proteins. Prediction of Type IV secreted proteins. Proteins involved in bacterial secretion systems. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. New release 5.0 of Eukaryotic-like domains finished. EffectiveDB-updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Prediction of microbial phenotypes based on comparative genomics.

effectivedb.org

New EffectiveT3 model | EffectiveDB

http://www.effectivedb.org/news/new-effectivet3-model

Dept of Microbiology and Ecosystem Science. A new prediction model for EffectiveT3 has been implemented. The new model 2.0 achieves better performance than the previous model 1.0 and is now available for job submission and for download. EffectiveDB-updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Prediction of microbial phenotypes based on comparative genomics. 43 1 4277 76681. 43 1 4277 876681. Contact.cube@univie.ac.at.

effectivedb.org

Imprint | EffectiveDB

http://www.effectivedb.org/imprint

Dept of Microbiology and Ecosystem Science. Division of Computational Systems Biology. Department of Microbiology and Ecosystem Science. Research Network "Chemistry meets Microbiology". EMAIL: contact.cube@univie.ac.at. PH: 43 1 4277 76681. FAX: 43 1 4277 876681. Disclaimer: The Division of Computational Systems Biology is responsible for the content of this website. The Division of Computational Systems Biology is not responsible for contents of external web pages. 43 1 4277 76681. 43 1 4277 876681.

old.vrvis.at

9th Imaging in the Life Sciences Meeting — VRVis

http://old.vrvis.at/frontpage/about/events/imaging-meeting

9th Imaging in the Life Sciences Meeting. Imaging meets Biomedical Image Informatics". Save the Date: June 2nd, 2016 - 1:30pm to 7pm. Hosted by VRVis @ Techgate Vienna. The Imaging in the Life Sciences Meeting is a regular meeting of the biomedical imaging community in Austria. It sparked to the creation of the recently established Correlated Multi Modal Imaging Node Austria. Please register until 30.5.2016 at: imaging-meeting@vrvis.at. Call for Posters and Software Demos:. Correlated Multi Modal Imaging...

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Computational Systems Biology, University of Vienna

Dept of Microbiology and Ecosystem Science. Bachelor and master projects. Our aim is to advance our understanding of biological systems,. Ranging from single species to multi-species systems and ecosystems,. Based on data from large-scale bioanalytical methods. We develop, improve and apply. For the interpretation of molecular information in biology. We establish and analyse. CUBE and friends BBQ on July 2. New webdesign for CUBE. The CUBE website has been redesigned based on a layout by pion. The Intrap...

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