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Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

Deprecated Software

2012 - 2015: OmixAnalyzer

The OmixAnalyzer is a web-based solution for integrated data management and analysis within large biomedical projects. A demo version of the software is available at the link above. It stores various types of processed microarray data (human, mouse, Affymetrix, Exon Chips, Agilent, etc.) and provides easy-to-use methods for quality control, clustering, and functional analysis of selected datasets.

The OmixAnalyzer was developed in the DFG-funded Collaborative Research Project (Sonderforschungsbereich / Transregio) TRR-54: Growth and Survival, Plasticity and Cellular Interactivity of Lymphatic Malignancies

Stoltmann, T., Zimmermann, K., Koschmieder, A. and Leser, U. (2013). OmixAnalyzer - A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets. Int. Conf. on Data Integration for the Life Sciences (DILS).

 


2012 - 2014: S4: Scalable String Similarity Search and Join Competition (link)

This competition addressed an important problem for database research and related fields, i.e., approximate string matching. Applications are many, such as duplicate detection, information extraction, error- tolerant keyword search etc. Participants of this workshop competed for the most efficient implementation of scalable approximate string matching techniques. The competition comprised two tracks: Similarity string search and similarity string join. The purpose was to get a clearer picture of the state-of-the-art in string matching by comparing algorithms using the same hardware and the same (large) data sets.

Results were presented at a workshop held in conjunction with EDBT/ICDT 2013, March 22, 2013, Genoa, Italy.

Wandelt, S., D. Deng, S. Gerdjikov, S. Mishra, P. Mitankin, M. Patil, E. Siragusa, A. Tiskin, W. Wang, J. Wang and U. Leser (2014). "State-of-the-art in String Similarity Search and Join." SIGMOD Record 43(1): 64-76.

 


2009 - today: CellFinder resources (link)

Resources that have been derived from the text mining experiments for the CellFinder project which aims to establishing a central stem cell data repository, by utilizing and interlinking existing public databases regarding defined areas of human pluripotent stem cell research.

These resources were developed within the DFG-funded research project CellFinder: A Cell Data Repository. CellFinder is still maintained by Charite Berlin.

Mariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf Leser (2012). Annotating and evaluating text for stem cell research, Third Workshop on Building and Evaluation Resources for Biomedical Text Mining.

 


2009 - 2011: PiPa (link)

PiPa is a tool to setup and maintain a local database for information on protein-protein interactions and biological pathways. It manages downloads and integration from a couple of public databases, including Reactome, BioCyc, BioGRID, GAD, MINT, IntAct, InHo, HPRD, PID, OMIM, MIPS, and UniProt. PiPa is not an application running on integrated data, but a tool to quickly create your own, in-house integrated database.

Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011). PiPa: Custom Integration of Protein Interactions and Pathways, Workshop "Daten In den Lebenswissenschaften".

 


2005 - 2013: Ali Baba (link)

Ali Baba is a software for extracting the most important information from all results of a PubMed search. Given a PubMed query, it collects all matching articles (using NCBI's eUtils), identifies all genes, diseases, drugs, species etc. plus their relationships to each each other in any of the articles, and displays these as a graph of interlinked biomedical concepts. Runs as a Java Web Start application.

Alibaba was developed and maintained between 2005 and 2013, but is no longer supported.

Plake, C., Schiemann, T., Pankalla, M., Hakenberg, J., and Leser, U. (2006). Ali Baba: PubMed as a graph, Bioinformatics, 22(19):2444-2445, 2006

 


2007 - 2013: PETER (link)

PETER is a library for DNA similarity search and joins. It indexes a large set of long DNA strings in a prefix-tree and allows for similarity searching using Hamming or edit-distance. Furthermore, two PETER indexes can be compared efficiently to perform a similarity join. Can be used as standalone tool, as a C++ library in other software, or as an extension for Oracle, thus allowing fast similarity operations with SQL.

PETER was developed and maintained from 2007 to 2011. The software is still available for download, but no longer supported.

Rheinländer, A., Knobloch, M., Hochmuth, N. and Leser, U. (2010). Prefix Tree Indexing for Similarity Search and Similarity Join on Genomic Data, Int. Conf. on Statistical and Scientific Databases, Heideberg, Germany.

 


2009 - 2012: LymphomExplorer

The LymphomExplorer is a web-based solution for integrated data management and analysis within large biomedical projects. It is developed in the course of the TRR-54 and funded by the Deutsche Forschungsgemeinschaft. It stores various types of processed microarray data (human, mouse, Affymetrix, Exon Chips, Agilent, etc.) and provides easy-to-use methods for quality control, clustering, and functional analysis of selected datasets.

The OmixAnalyzer was developed in the DFG-funded Collaborative Research Project (Sonderforschungsbereich / Transregio) TRR-54: Growth and Survival, Plasticity and Cellular Interactivity of Lymphatic Malignancies

LyphomExplorer was developed and maintained between 2009 and 2012. Please see our new tool OmixAnalyzer.

Stoltmann, T., Zimmermann, K., Koschmieder, A. and Leser, U.
OmixAnalyzer: A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets
Int. Conf. on Data Integration for the Life Sciences, Montreal, Canada, 2013.

 


2008 - 2011: BC-Viscon

The BC-VisCon website provides an intuitive and flexible tool for viewing and analyzing aggregations and comparisons of the annotations made by the gene mention tagging servers connected to the BioCreAtIve-MetaServer.

BC-Viscon was maintained between 2008 and 2011.

Starlinger, J., Leitner, F., Valencia, A. and Leser, U. (2009). SOA-based Integration of Text Mining Services, Int Conf. on Web Services, Los Angeles, US.

 


2006 - 2008: DARQ (link)

DARQ is a query engine for federated SPARQL queries. It provides transparent query access to multiple, distributed SPARQL endpoints as if querying a single RDF graph. DARQ enables the applications to see a single query interface, leaving the details of federation to the query engine.

DARQ was developed in the course of the Graduate School METRIK, funded by the Deutsche Forschungsgemeinschaft.

Quilitz, B. and Leser, U. (2008). Querying Distributed RDF Data Sources with SPARQL, European Semantic Web Conference, Teneriffa, Spain.