159 Works

A case study for efficient management of high throughput primary lab data

Christian Colmsee, Steffen Flemming, Matthias Klapperstück, Matthias Lange & Uwe Scholz
Source code for the LimsLight primary data management system

Visualising comparative genomics with Hilbert curves

Thomas Schmutzer, Fabian Bull & Uwe Scholz
Poster - Bioinformatics of Human and Animal Genomics 2011

IDPredictor: predict database links in biomedical database

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Supplementary material A.3 for the paper 'IDPredictor: predict database links in biomedical database'. Abstract: Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data are spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab...

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 1 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 2 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

Physiologische und bioanalytische Untersuchungen während der Pollenembryogenese von Hordeum vulgare

Rico Lippmann
Vergelichende Proteinanalyse ("shot gun") zwischen Pollenembryogenese nach Kältestress-Induktion und gametophytischer Entwicklung von Hordeum vulgare. Replikat 3 der Untersuchung. Nach tryptischen Verdaus erfolgte die Trennung auf einer RP18-Säule (BEH 1,7µm, 100 mm x 100 µm) gekoppelt an eine RP-18 Vorsäule (Symmetry 5µm, 20mm x 180 µm) an einer nanoLC-ESI-QTOF-MS/MS (Waters) modifiziert nach Kaspar et al. (2010). Die Auswertung der Daten Eine weitere Auswertung der Chromatogramme wurde mit dem Programm LC-MS Progenesis (Nonlinear, Großbritannien) durchgeführt.

IDPredictor: predict database links in biomedical database

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Abstract: Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data are spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a...

Poster_BIT_IPK-Evaluation_2012

Uwe Scholz
Poster_BIT_IPK-Evaluation_2012

Poster_DI_IPK-Evaluation_2012

Swetlana Friedel
Poster_DI_IPK-Evaluation_2012

Poster_The LAILAPS Search Engine: New Features

Jinbo Chen
LAILAPS Poster für IB 2012

Distribution of ASCII characters in Database IDs

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Distribution of character frequency in sample of 51,000 IDs from 51 biomedical databases: The three columns show the ASCII code of the character, the printable form and the frequency of occurence. We hide the ASCII codes 128 - 255, because they never showed up in the sample IDs. Overall we see 182 characters do not show up in any ID (54 in the range of frequently used 7-bit ASCII subset)

Prediction performance for UniProt entry CP20C ARATH

Matthias Lange, Hendrik Mehlhorn, Uwe Scholz & Falk Schreiber
Evaluation of the IDPredictor ID classifier in the UniProt entry CP20C ARATH. The columns are: extracted token, predicted database cross-reference, p-value, manual evaluation (1: true posive; 0: false positive). Overall we decomposed the entry into 1,803 tokens. The table comprise only those 531 tokens which had a minimal p-value of 0.5.

Processed raw data as used for the quantitative analysis of the response of the barley root plasma membrane to salinity stress

Katja Witzel
Processed raw data as used for the quantitative analysis of the response of the barley root plasma membrane to salinity stress. Three replicates were analyzed for both each treatment and each genotype. Proteins were either digested with trypsin or elastase. Protein separation was performed by means of reversed phase chromatography on a BEH 130 column (1,7µm, 100 mm x 100 µm) coupled to a trap column for desalting (Symmetry 5µm, 20mm x 180 µm) and...

The e!DAL JAVA-API - Store, Share and Cite Primary Data in Life Sciences

Daniel Arend
Current strategies for primary data management towards effective data publication, retrieval, sharing and citation require enhanced platforms. One driving force is the recent developments in biotechnology. It is attended by a strong growth of scientific primary data. For example, “Next-Generation-Sequencing” or “Plant-Phenotyping” technologies produce a huge amount of primary data. Its analysis and publication is one pillar in modern life science research. Consequently, the responsible use and efficient availability of digital resources is an important...

The e!DAL JAVA-API - Store, Share and Cite Primary Data in Life Sciences

Daniel Arend
Current strategies for primary data management towards effective data publication, retrieval, sharing and citation require enhanced platforms. One driving force is the recent developments in biotechnology. It is attended by a strong growth of scientific primary data. For example, “Next-Generation-Sequencing” or “Plant-Phenotyping” technologies produce a huge amount of primary data. Its analysis and publication is one pillar in modern life science research. Consequently, the responsible use and efficient availability of digital resources is an important...

The e!DAL JAVA-API: Store, Share and Cite Primary Data in Life Sciences

Daniel Arend
Current strategies for primary data management towards effective data publication, retrieval, sharing and citation require enhanced platforms. One driving force is the recent developments in biotechnology. It is attended by a strong growth of scientific primary data. For example, “Next-Generation-Sequencing” or “Plant-Phenotyping” technologies produce a huge amount of primary data. Its analysis and publication is one pillar in modern life science research. Consequently, the responsible use and efficient availability of digital resources is an important...

Three-dimensional model of airspaces in the developing Brassica napus seed

Pieter Verboeven
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. Out of the reconstructed cross-section images (1500 virtual sections), the three-dimensional model of the void network in the developing seed of Brassica napus was generated. Developmental stage corresponds to the main storage phase (about 30 days after fertilization).

Animated movie of the high-resolution CT images of the developing Brassica napus seed

Pieter Verboeven
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. The X-ray shadow projections of the 3-D object were digitized as 2048 x 2048 pixel images and were processed to obtain reconstructed cross-section images using a mathematical algorithm based on the filtered back-projection procedure implemented in the NRecon 1.6.2.0 software. This resulted in a 3-D stack of 1500 virtual sections, each consisting of 1500 × 1500 isotropic voxels of (1.7 µm3) with a linear...

Micro CT raw data as used for the imaging of the void network in Brassica napus

Pieter Verboeven
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. The X-ray shadow projections of the 3-D object were digitized and processed to obtain reconstructed cross-section images. This resulted in a 3-D stack of 1500 virtual sections, each consisting of 1500 × 1500 isotropic voxels of (1.7 µm). These data were subsequently used to model the void network in the developing seed of Brassica napus and to calculate the apparent diffusivities. Developmental stage corresponds...

Acquired raw data as used for the protein identification of differential spots from the quantitative analysis of the response of the barley root proteome to salinity stress

Katja Witzel
Acquired raw data as used for the protein identification of differential spots from the quantitative analysis of the response of the barley root proteome to salinity stress. Acquisition of peptide mass fingerprint data was performed on a Reflex III MALDI-TOF device (Bruker Daltonics, Bremen, Germany, www.bruker.com/) operating in reflector mode using the FlexControl software. Spectra were calibrated using external calibration, with subsequent internal mass correction. Protein identification was performed with the Mascot search engine (Matrix...

Supporting material for the article "A sequence-ready physical map of barley anchored genetically by two million SNPs"

Martin Mascher
Barley (Hordeum vulgare L.) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion base pair genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes (BACs) representing 14x haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96 % of the...

DPPN Techno: manage, analyse, share and publish phenotype data

Daniel Arend, Wolfgang Zu Castell, Elisabeth Georgii, Igor Grigoriev, Matthias Lange, Anton Schaffner, Uwe Scholz & Björn Usadel
The DPPN collaboration project, started in 2012, develops new concepts and technologies in the field of high-throughput plant phenotyping, yielding a huge amount of data on physical and biochemical traits of plant organisms. The DPPN Techno module hosted by the three partner institutes - IPK Gatersleben, Helmholtz Zentrum München and Forschungszentrum Jülich - deals with planning, establishment and extension of the IT infrastructures for storage, management, analysis and publication of phenotypic data and their integration...

Spelling correction of TAIR queries using query user refinement which has been recorded in query logs.

Jinbo Chen
List of 2740 corrected words, which where extracted form TAIT query logs based on their relationship to a user session.

Supplemental material : 'Isoprene emission-free poplars - a chance to reduce the impact from poplar plantations on the atmosphere

Jörg-Peter Schnitzler
Depending on the atmospheric composition, isoprene emissions from plants can have a severe impact on air quality and regional climate. For the plant itself, isoprene can enhance stress tolerance and also interfere with the attraction of herbivores and parasitoids. Here, we tested the growth performance and fitness of Populus á canescens in which iso-prene emission had been knocked down by RNA interference technology (PcISPS-RNAi plants) for two growing seasons under outdoor conditions. Neither the growth...

Reference set of relevance ranked plant traits

Eva Grafahrend-Belau
Relevance ranking training for trait queries: The crucial step for the search engine training is a set of true positive relevance rankings. In order to express the relevance of a database entry, a manual set of 400 relevance rated database entries curated for 20 queries over 6 trait categories has been performed.round with user profiles and profile specific relevance criteria. To combine end user and domain expert knowledge, use cases, which have a common general...

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