Abstract:
BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability. RESULTS:We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform. CONCLUSIONS:Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SYdoi
10.1186/s12859-020-03928-1subject
Has Abstractpub_date
2020-12-17 00:00:00pages
582issue
1issn
1471-2105pii
10.1186/s12859-020-03928-1journal_volume
21pub_type
杂志文章abstract:BACKGROUND:With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to sc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2642-7
更新日期:2019-02-18 00:00:00
abstract:BACKGROUND:An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1865-8
更新日期:2017-10-23 00:00:00
abstract:BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-344
更新日期:2010-06-24 00:00:00
abstract:BACKGROUND:To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3407-z
更新日期:2020-02-17 00:00:00
abstract:BACKGROUND:Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the pas...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3114-9
更新日期:2019-10-30 00:00:00
abstract:BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-314
更新日期:2013-10-28 00:00:00
abstract::Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S17-I1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-101
更新日期:2004-07-26 00:00:00
abstract:BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S11-S16
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discreti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-520
更新日期:2010-10-19 00:00:00
abstract:BACKGROUND:Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have bee...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-21
更新日期:2007-01-23 00:00:00
abstract:BACKGROUND:Computer-aided segmentation and border detection in dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermoscopy images have become an important research field mainly because of inter- and intra-observer var...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S6-S26
更新日期:2010-10-07 00:00:00
abstract:BACKGROUND:Gene expression patterns of olfactory receptors (ORs) are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD) to house OR gene exp...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-231
更新日期:2007-06-30 00:00:00
abstract:BACKGROUND:Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-37
更新日期:2005-02-23 00:00:00
abstract:BACKGROUND:Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexibl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-97
更新日期:2009-03-27 00:00:00
abstract:BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3015-y
更新日期:2019-08-15 00:00:00
abstract:BACKGROUND:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various sample...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-106
更新日期:2006-03-02 00:00:00
abstract:BACKGROUND:Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are di...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-S16-S11
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known bindi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S7-S11
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-3-11
更新日期:2002-04-23 00:00:00
abstract:BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-66
更新日期:2009-02-20 00:00:00
abstract:BACKGROUND:Biologists often conduct multiple but different cDNA microarray studies that all target the same biological system or pathway. Within each study, replicate slides within repeated identical experiments are often produced. Pooling information across studies can help more accurately identify true target genes. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-247
更新日期:2006-05-05 00:00:00
abstract:BACKGROUND:The structure conservation in various α-helix subclasses reveals the sequence and context dependent factors causing distortions in the α-helix. The sequence-structure relationship in these subclasses can be used to predict structural variations in α-helix purely based on its sequence. We train support vector...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S20
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1473-7
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2412-y
更新日期:2018-11-14 00:00:00
abstract:BACKGROUND:The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-19
更新日期:2005-01-27 00:00:00
abstract:BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-229
更新日期:2010-05-06 00:00:00
abstract:BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2353-5
更新日期:2018-10-04 00:00:00
abstract:BACKGROUND:Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3085-x
更新日期:2019-12-02 00:00:00