The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312015 | PMC |
| http://dx.doi.org/10.1002/0471250953.bi0312s48 | DOI Listing |
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Highly parallel simulation tool for the design of isotachophoresis experiments.
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Department of Mechanical Engineering, Stanford University, 488 Escondido Mall, Stanford, CA, 94305, USA. Electronic address:
Background: Isotachophoresis (ITP) is a well-established electrokinetic method for separation and preconcentration of analytes. Several simulation tools for ITP have been published, but their use for experimental design is limited by the computational time for a single run and/or by the number of conditions that can be investigated per simulation run. A large fraction of the existing solvers also do not account for ionic strength effects, which can influence whether an analyte focuses in ITP.
View Article and Find Full Text PDFUnipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides.
J Proteome Res
January 2025
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.
Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From the onset, Unipept's capabilities focused on tryptic peptides, utilizing the predictability and consistency of trypsin digestion to efficiently construct a protein reference database. However, the evolving landscape of proteomics and emerging fields like immunopeptidomics necessitate a more versatile approach that extends beyond the analysis of tryptic peptides.
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Strahlenther Onkol
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Department of Radiation Oncology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
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AutoGP: An Intelligent Breeding Platform for Enhancing Maize Genomic Selection.
Plant Commun
January 2025
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Hubei, China. Electronic address:
In the face of climate change and the growing global population, there is an urgent need to accelerate the development of high-yielding crop varieties. To this end, vast amounts of genotype-to-phenotype data have been collected, and many machine learning (ML) models have been developed to predict phenotype from a given genotype. However, the requirement for high densities of single-nucleotide polymorphisms (SNPs) and the labor-intensive collection of phenotypic data are hampering the use of these models to advance breeding.
View Article and Find Full Text PDFExploratory multivariate analysis using R Language for method development in liquid chromatography.
Anal Bioanal Chem
January 2025
Department of Medical Biochemistry, Faculty of Medicine in Hradec Králové, Charles University, Šimkova 870, 500 03, Hradec Králové, Czech Republic.
The visual evaluation of data derived from screening and optimization experiments in the development of new analytical methods poses a considerable time investment and introduces the risk of subjectivity. This study presents a novel approach to processing such data, based on factor analysis of mixed data and hierarchical clustering - multivariate techniques implemented in the R programming language. The methodology is demonstrated in the early-stage screening and optimization of the chromatographic separation of 15 structurally diverse drugs that affect the central nervous system, using a custom R Language script.
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