Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Applications in computer-assisted biology
    Nijveen, H. - \ 2013
    Wageningen University. Promotor(en): Ton Bisseling, co-promotor(en): P.E. van der Vet. - Wageningen : Wageningen UR - ISBN 9789461737816 - 106
    bio-informatica - moleculaire biologie - computers - databanken - prokaryoten - computeranalyse - informatietechnologie - bioinformatics - molecular biology - computers - databases - prokaryotes - computer analysis - information technology

    Biology is becoming a data-rich science driven by the development of high-throughput technologies like next-generation DNA sequencing. This is fundamentally changing biological research. The genome sequences of many species are becoming available, as well as the genetic variation within a species, and the activity of the genes in a genome under various conditions. With the opportunities that these new technologies offer, comes the challenge to effectively deal with the large volumes of data that they produce. Bioinformaticians have an important role to play in organising and analysing this data to extract biological information and gain knowledge. Also for experimental biologists computers have become essential tools. This has created a strong need for software applications aimed at biological research. The chapters in this thesis detail my contributions to this area. Together with molecular biologists, plant breeders, immunologists, and microbiologists, I have developed several software tools and performed computational analyses to study biological questions.

    Chapter 2 is about Primer3Plus, a web tool that helps biologists to design DNA primers for their experiments. These primers are typically short stretches of DNA (~20 nucleotides) that direct the DNA replication machinery to copy a selected region of a DNA molecule. The specificity of a primer is determined by several chemical and physical properties and therefore designing good primers is best done with the help of a computer program. Primer3Plus offers a user-friendly task-oriented web interface to the popular primer3 primer design program. Primer3Plus clearly fulfils a need in the biological research community as already over 400 scientific articles have cited the Primer3Plus publication.

    Single nucleotide differences or polymorphisms (SNPs) that are present within a species can be used as markers to link phenotypic observations to locations on the genome. Chapter 3 discusses QualitySNPng, which is a stand-alone software tool for finding SNPs in high-throughput sequencing data. QualitySNPng was inspired by the QualitySNP pipeline for SNP detection that was published in 2006 and it uses similar filtering criteria to distinguish SNPs from technical artefacts like sequence read errors. In addition, the SNPs are used to predict haplotypes. QualitySNPng has a graphical user interface that allows the user to run the SNP detection and evaluate the results. It has already been successfully used in several projects on marker detection for plant breeding.

    Single nucleotide polymorphisms can lead to single amino acid changes in protein sequences. These single amino acid polymorphisms (SAPs) play a key role in graft-versus-host (GVH) effects that often accompany tissue transplantations. A beneficial variant of GVH is the graft-versus-leukaemia (GVL) effect that is sometimes witnessed after bone marrow transplantation in leukaemia patients. When the GVL effect occurs, the donor’s immune cells actively destroy residual tumour cells in the patient. The GVL effect can already be elicited by a single amino acid difference between the patient and the donor. Currently, a small number of SAPs that can elicit a GVL effect are known and these are used to select the right bone marrow donor for a leukaemia patient. Together with researchers at the Leiden University Medical Center I developed a database to aid in the discovery of more such SAPs. We called this database the “Human Short Peptide Variation database” or HSPVdb. It is described in chapter 4.

    The work described in chapter 5 is focused on the regions in bacterial genomes that are involved in gene regulation, the promoters. Intrigued by anecdotal evidence that duplication of bacterial promoters can activate or silence genes, we investigated how often promoter duplication occurs in bacterial genomes. Using the large number of bacterial genomes that are currently available, we looked for clusters of highly similar promoter regions. Since duplication assumes some sort of mobility, we termed the duplicated promoters: putative mobile promoters or PMPs. We found over 4,000 clusters of PMPs in 1,043 genomes. Most of the clusters consist of two members, indicating a single duplication event, but we also found much larger clusters of PMPs within some genomes. A number of PMPs are present in multiple species, even in very distantly related bacterial species, suggesting perhaps that these were subjected to horizontal gene transfer. The mobile promoters could play an important role in the rapid rewiring of gene regulatory networks.

    Chapter 6 discusses how current biological research can adapt to make full use of the opportunities offered by the high-throughput technologies by following three different approaches. The first approach empowers the biologists with user-friendly software that allows him to analyse the large volumes of genome scale data without requiring expert computer skills. In the second approach the biologist teams up with a bioinformatician to combine in-depth biological knowledge with expert computational skills. The third approach combines the biologist and the bioinformatician in one person by teaching the biologist computational skills. Each of these three approaches has it merits and shortcomings, so I do not expect any of them to become dominant in the near future. Looking further ahead, it seems inevitable that any biologist will have to learn at least the basics of computational methods and that this should be an integral part of biology education. Bioinformatics might in time cease to exist as a separate field and instead become an intrinsic aspect of most biological research disciplines.

    Energiebesparing varkens : slimme klimaatcomputer de baas blijven
    Animal Sciences Group (ASG), - \ 2012
    Lelystad : Animal Sciences Group Wageningen UR, Business Unit Veehouderij
    varkenshouderij - varkensstallen - stalklimaat - energiebesparing - computers - ventilatie - pig farming - pig housing - stall climate - energy saving - computers - ventilation
    Klimaatcomputers bieden zeer uitgebreide mogelijkheden om het stalklimaat te regelen. Dit is tegelijk de beperking van deze apparatuur. Door de complexiteit zie je snel zaken over het hoofd en bestaat het risico dat regelmatig controleren en bijstellen van ingestelde waardes achterwege blijft. Een regelmatige controle door een klimaatspecialist helpt om de klimaatcomputer en het stalklimaat bij de tijd te houden.
    Systems Biology and Livestock Science
    Pas, M.F.W. te; Woelders, H. ; Bannink, A. - \ 2011
    Chichester, UK : John Wiley and Sons - ISBN 9780813811741 - 332
    dieren - systeembiologie - vee - computers - moleculaire biologie - animals - systems biology - livestock - computers - molecular biology
    Systems Biology is an interdisciplinary approach to the study of life made possible through the explosion of molecular data made available through the genome revolution and the simultaneous development of computational technologies that allow us to interpret these large data sets. Systems Biology has changed the way biological science views and studies life and has been implemented in research efforts across the biological sciences. Systems Biology and Livestock Science will be the first book to review the latest advances using this research methodology in efforts to improve the efficiency, health, and quality of livestock production. Systems Biology and Livestock Science opens with useful introductory chapters explaining key systems biology principles. The chapters then progress to look at specific advances in fields across livestock science. Coverage includes, but is not limited to, chapters on systems biology approaches to animal nutrition, reproduction, health and disease, and animal physiology. Written by leading researchers in the field, Systems Biology and Livestock Science, will be an invaluable resource to researchers, professionals, and advance students working in this rapidly developing discipline.
    PocketGEO/Sampview: software for nematode sampling
    Been, T.H. ; Spätjens, L.E.E.M. - \ 2010
    - p. 115 - 115.
    precisielandbouw - bemonsteren - computers - handgereedschap - geografische informatiesystemen - grondanalyse - nematodenbestrijding - gewasbescherming - vrijlevende nematoden - precision agriculture - sampling - computers - hand tools - geographical information systems - soil analysis - nematode control - plant protection - free living nematodes
    PocketGeo/SampView is a software program for soil sampling agencies. It will run on any handheld PDA and can be used in the field by the soil sampler. The program can divide farmer fields on site into an optimized set of areas to be sampled according to the restraints given by the chosen sampling method.
    ICT in Dutch Horticulture: State of the Art and Future Challenges [poster]
    Verdouw, C.N. ; Wolfert, J. ; Beulens, A.J.M. ; Ravensbergen, P. - \ 2010
    computers - computertechnieken - tuinbouw - innovaties - informatietechnologie - computational science - computers - computer techniques - horticulture - innovations - information technology - computational science
    Poster over Informatie- en Communicatie Technologie in de Nederlandse tuinbouw: Hoever zijn we en wat zijn de uitdagingen voor de toekomst.
    A knowledge-intensive approach to computer vision systems
    Koenderink, N.J.J.P. - \ 2010
    Delft University of Technology. Promotor(en): L.J. van Vliet; Jan Top. - S.l. : s.n. - ISBN 9789085855644 - 173
    machine vision - beeldanalyse - beeldverwerking - kwaliteitscontroles - inspectie - computers - modellen - kennissystemen - modelleren - machine vision - image analysis - image processing - quality controls - inspection - computers - models - knowledge systems - modeling
    Web services for transcriptomics
    Neerincx, P. - \ 2009
    Wageningen University. Promotor(en): Jack Leunissen. - [S.l. : S.n. - ISBN 9789085854647 - 184
    bio-informatica - internet - moleculaire biologie - computers - datacommunicatie - gegevensverwerking - transcriptomics - computernetwerken - microarrays - genexpressieanalyse - datamining - bioinformatics - internet - molecular biology - computers - data communication - data processing - transcriptomics - computer networks - microarrays - genomics - data mining
    Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as messenger molecules containing a copy of the genetic code, which can be used by the ribosomes as templates to synthesise proteins. Over the past decade microarray technology has become the dominant technology for performing high throughput gene expression experiments.
    A microarray contains short sequences (oligos or probes), which are the reverse complement of fragments of the targets (transcripts or sequences derived thereof). When genes are expressed, their transcripts (or sequences derived thereof) can hybridise to these probes. Many thousand copies of a probe are immobilised in a small region on a support. These regions are called spots and a typical microarray contains thousands or sometimes even more than a million spots. When the transcripts (or sequences derived thereof) are fluorescently labelled and it is known which spots are located where on the support, a fluorescent signal in a certain region represents expression of a certain gene. For interpretation of microarray data it is essential to make sure the oligos are specific for their targets. Hence for proper probe design one needs to know all transcripts that may be expressed and how well they can hybridise with candidate oligos. Therefore oligo design requires:
    1. A complete reference genome assembly.
    2. Complete annotation of the genome to know which parts may be transcribed.
    3. Insight in the amount of natural variation in the genomes of different individuals.
    4. Knowledge on how experimental conditions influence the ability of probes to hybridise with certain transcripts.
    Unfortunately such complete information does not exist, but many microarrays were designed based on incomplete data nevertheless. This can lead to a variety of problems including cross-hybridisation (non-specific binding), erroneously annotated and therefore misleading probes, missing probes and orphan probes.
    Fortunately the amount of information on genes and their transcripts increases rapidly. Therefore, it is possible to improve the reliability of microarray data analysis by regular updates of the probe annotation using updated databases for genomes and their annotation. Several tools have been developed for this purpose, but these either used simplistic annotation strategies or did not support our species and/ or microarray platforms of interest. Therefore, we developed OligoRAP (Oligo Re- Annotation Pipeline), which is described in chapter 2. OligoRAP was designed to take advantage of amongst others annotation provided by Ensembl, which is the largest genome annotation effort in the world. Thereby OligoRAP supports most of the major animal model organisms including farm animals like chicken and cow. In addition to support for our species and array platforms of interest OligoRAP employs a new annotation strategy combining information from genome and transcript databases in a non-redundant way to get the most complete annotation possible.
    In chapter 3 we compared annotation generated with 3 oligo annotation pipelines including OligoRAP and investigated the effect on functional analysis of a microarray experiment involving chickens infected with Eimeria bacteria. As an example of functional analysis we investigated if up- or downregulated genes were enriched for Terms from the Gene Ontology (GO). We discovered that small differences in annotation strategy could lead to alarmingly large differences in enriched GO terms.
    Therefore it is important to know, which annotation strategy works best, but it was not possible to assess this due to the lack of a good reference or benchmark dataset. There are a few limited studies investigating the hybridisation potential of imperfect alignments of oligos with potential targets, but in general such data is scarce. In addition it is difficult to compare these studies due to differences in experimental setup including different hybridisation temperatures and different probe lengths. As result we cannot determine exact thresholds for the alignments of oligos with non-targets to prevent cross-hybridisation, but from these different studies we can get an idea of the range for the thresholds that would be required for optimal target specificity. Note that in these studies experimental conditions were first optimised for an optimal signal to noise ratio for hybridisation of oligos with targets. Then these conditions were used to determine the thresholds for alignments of oligos with non-targets to prevent cross-hybridisation.
    Chapter 4 describes a parameter sweep using OligoRAP to explore hybridisation potential thresholds from a different perspective. Given the mouse genome thresholds were determined for the largest amount of gene specific probes. Using those thresholds we then determined thresholds for optimal signal to noise ratios. Unfortunately the annotation-based thresholds we found did not fall within the range of experimentally determined thresholds; in fact they were not even close. Hence what was experimentally determined to be optimal for the technology was not in sync with what was determined to be optimal for the mouse genome. Further research will be required to determine whether microarray technology can be modified in such a way that it is better suited for gene expression experiments. The requirement of a priori information on possible targets and the lack of sufficient knowledge on how experimental conditions influence hybridisation potential can be considered the Achiles’ heels of microarray technology.
    Chapter 5 is a collection of 3 application notes describing other tools that can aid in analysis of transcriptomics data. Firstly, RShell, which is a plugin for the Taverna workbench allowing users to execute statistical computations remotely on R-servers. Secondly, MADMAX services, which provide quality control and normalisation of microarray data for AffyMetrix arrays. Finally, GeneIlluminator, which is a tool to disambiguate gene symbols allowing researchers to specifically retrieve literature for their genes of interest even if the gene symbols for those genes had many synonyms and homonyms.

    Web services

    High throughput experiments like those performed in transcriptomics usually require subsequent analysis with many different tools to make biological sense of the data. Installing all these tools on a single, local computer and making them compatible so users can build analysis pipelines can be very cumbersome. Therefore distributed analysis strategies have been explored extensively over the past decades. In a distributed system providers offer remote access to tools and data via the Internet allowing users to create pipelines from modules from all over the globe.
    Chapter 1 provides an overview of the evolution of web services, which represent the latest breed in technology for creating distributed systems. The major advantage of web services over older technology is that web services are programming language independent, Internet communication protocol independent and operating system independent. Therefore web services are very flexible and most of them are firewall-proof. Web services play a major role in the remaining chapters of this thesis: OligoRAP is a workflow entirely made from web services and the tools described in chapter 5 all provide remote programmatic access via web service interfaces. Although web services can be used to build relatively complex workflows like OligoRAP, a lack of mainly de facto standards and of user-friendly clients has limited the use of web services to bioinformaticians. A semantic web where biologists can easily link web services into complex workflows does n
    Computermodel leidt tot beter bemesten en water geven : systeem voor biotelers gemakkelijk te vertalen naar gangbare grondteelt(interview met Pieter de Visser)
    Kierkels, T. ; Visser, P.H.B. de - \ 2009
    Onder Glas 6 (2009)1. - p. 68 - 69.
    tuinbouw - teelt onder bescherming - bodemvruchtbaarheid - computers - automatisering - informatiesystemen - mest - bloementeelt - glastuinbouw - bodemkwaliteit - bemesting - glasgroenten - groenten - snijbloemen - horticulture - protected cultivation - soil fertility - computers - automation - information systems - manures - floriculture - greenhouse horticulture - soil quality - fertilizer application - greenhouse vegetables - vegetables - cut flowers
    Het Bodemmanagement-Informatiesysteem voor de biologische glastuinbouw is klaar voor de praktijk. Met simpele aanpassingen is het ook voor gangbare grondtelers geschikt te maken. Het model geeft veel inzicht in opname en uitspoeling van meststoffen. Beslissingen over hoeveelheden meststoffen, bemestingsmomenten en water gift zijn gefundeerder te maken. Dat kan geld besparen
    Een camera kan niet alles
    Zedde, Rick van de - \ 2008
    horticulture - greenhouses - video cameras - phalaenopsis - computer software - computers - computer techniques - image analysis - sorting - greenhouse horticulture
    Geavanceerde computerondersteuning van kwantitatief onderzoek
    Rijgersberg, H. ; Top, J.L. ; Wigham, M.L.I. - \ 2008
    Agro Informatica 21 (2008)4. - ISSN 0925-4455 - p. 15 - 17.
    onderzoeksondersteuning - computers - organisatie van onderzoek - wetenschappelijk onderzoek - research support - computers - organization of research - scientific research
    Kwantitatief onderzoek vindt in belangrijke mate op de computer plaats. Toch is de computerondersteuning van kwantitatief onderzoek niet ideaal. Er zijn meerdere, ongekoppelde systemen nodig en veel informatie blijft impliciet en dus niet toegankelijk voor automatische verwerking. De oplossing schuilt in semantische ontsluiting van de kwantitatieve informatie. Daartoe werd een kwantitatief vocabulaire ontwikkeld, die daarna werd toegepast in ontwikkelde tools, waarna het gebruik van deze tools met kwantitatieve onderzoekers werd geëvalueerd
    Mensen in beweging: het gebruik van "tracking" gegevens binnen de ruimtelijke planvorming
    Ligtenberg, A. - \ 2008
    Agro Informatica 21 (2008)2. - ISSN 0925-4455 - p. 7 - 9.
    informatietechnologie - informatiewetenschap - globale plaatsbepalingssystemen - detectie - voortbeweging - computers - analyse - recreatie - geoinformatie - information technology - information science - global positioning systems - detection - locomotion - computers - analysis - recreation - geoinformation
    In dit artikel wordt een kort overzicht gegeven van de verschillende activiteiten die binnen deze projecten plaatsvinden. Begonnen wordt met een korte uitleg van een aantal basisconcepten en vervolgens zal een casestudie rondom een toepassing voor het analyseren van recreatie in natuurgebieden worden gepresenteerd
    Kijk in de kas: een interactieve leeromgeving voor telers (interview met Fokke Buwalda)
    Arkesteijn, M. ; Buwalda, F. - \ 2008
    Onder Glas 5 (2008)1. - p. 36 - 37.
    tuinbouwbedrijven - kassen - teelt onder bescherming - onderzoek - verspreiding van onderzoek - informatieverspreiding - computers - glastuinbouw - kennisoverdracht - computernetwerken - market gardens - greenhouses - protected cultivation - research - diffusion of research - diffusion of information - computers - greenhouse horticulture - knowledge transfer - computer networks
    De webportal Kijk in de Kas is een interactief instrument om praktijk- en onderzoekskennis uit te wisselen. Teler kunnen een virtueel kijkje nemen bij vijf collega's. Klimaatmodel KASPRO rekent mee en produceert mooie plaatjes. De betrokken onderzoekers en telers geven via weblogs hun commentaar. Ze streven op deze manier naar een betere koppeling van onderzoek en praktijk op het gebied van de energiebesparing
    A computer model for welfare assessment of poultry production systems for laying hens
    Mol, R. de; Schouten, W.G.P. ; Evers, A.G. ; Houwers, H.W.J. - \ 2006
    NJAS Wageningen Journal of Life Sciences 54 (2006)2. - ISSN 1573-5214 - p. 157 - 168.
    pluimveehouderij - hennen - huisvesting, dieren - diergezondheid - dierenwelzijn - modellen - computers - analyse - scharrelhouderij - agrarische productiesystemen - poultry farming - hens - animal housing - animal health - animal welfare - models - computers - analysis - free range husbandry - agricultural production systems
    A computer model for welfare assessment in laying hens was constructed. This model, named FOWEL (fowl welfare), uses a description of the production system as input and produces a welfare score as output. To assess the welfare status a formalized procedure based on scientific knowledge is applied. In FOWEL the production system is described using 25 attributes (space per hen, beak trimming, free range, etc.), each with two or more levels, together defining the characteristics of a production system. A weighting factor is used for each attribute, based on the available scientific knowledge of the effects of the attribute levels on the welfare aspects. The welfare score of a production system results from the attribute levels combined with the weighting factors. The results show that feeding level, space per hen, perches, water availability and nests were the most important attributes. The attribute free range was of minor importance. FOWEL includes a description of 22 production systems. The welfare score of cage systems was low, of barn and aviary systems medium, and of organic systems high. The presence of a free range resulted only in a small improvement in the welfare score.
    Meting van ruimtelijke verdeling van temperatuur en RV met behulp van draadloze minisensoren (Smart Dust). Deel 1 : Programma van wensen en eisen voor het on-line meten van de ruimtelijke verdeling van temperatuur en RV met draadloze minisensoren
    Os, E.A. van; Bruins, M.A. ; Tuijl, B.A.J. van - \ 2006
    Wageningen : Plant Research International (Rapport / Plant Research International 126) - 33
    kassen - milieufactoren - temperatuur - relatieve vochtigheid - monitoring - gegevens verzamelen - computers - glastuinbouw - greenhouses - environmental factors - temperature - relative humidity - monitoring - data collection - computers - greenhouse horticulture
    De ruimtelijke verdeling van de kasluchttemperatuur en de relatieve vochtigheid is niet gelijk. Door de verschillen ontstaan koude en warme plekken in de kas, maar kunnen ook ziekten en onregelmatige groei van het gewas optreden. In deze studie wordt verslag gedaan van een inventarisatie onder onderzoekers en telers naar de behoefte aan een on-line draadloos meetsysteem bestaande uit minisensoren waardoor klimaatverschillen gemakkelijker zijn op te sporen
    Modelling Trade and Trust across Cultures
    Hofstede, G.J. ; Jonker, C.M. ; Meijer, S.A. ; Verwaart, D. - \ 2006
    In: Trust Management: 4th International Conference, iTrust 2006: Proceedings, Pisa, Italy, May 16-19, 2006. - Berlin Heidelberg : Spinger Verlag (Lecture notes in computer science 3986) - ISBN 9783540342953 - p. 120 - 134.
    computers - samenleving - informatieontsluiting - informatieopslag - informatiesystemen - internet - computerwetenschappen - computernetwerken - computers - society - information retrieval - information storage - information systems - internet - computer sciences - computer networks
    Misunderstandings arise in international trade due to difference in cultural background of trade partners. Trust and the role it plays in trade are influenced by culture. Considering that trade always invloves working on the relationship with the trade partner, understanding the behaviour of the other is of the essence. This paper proposes to involve cultural dimensions in the modelling of trust in trade situations. A case study is presented to show a conceptualisation of trust with respect to the cultural dimension of performance orientation versus cooperation.
    Betere afstemming vraag en aanbod van stikstof mogelijk met telersversie Ndicea
    Dijk, W. van; Burgt, G.J.H.M. van der - \ 2005 2005 (2005)15 nov.
    stikstofmeststoffen - computeranalyse - statistische analyse - computers - rotaties - teeltsystemen - akkerbouw - bemesting - nitrogen fertilizers - computer analysis - statistical analysis - rotations - cropping systems - arable farming - fertilizer application
    Van het computermodel Ndicea was al een gebruiksvriendelijke versie beschikbaar die door telers zonder begeleiding ingezet kan worden. Deze versie NDICEA Vruchtwisseling is echter alleen geschikt voor berekeningen op niveau van de vruchtwisseling (strategische keuzes bedrijfsvoering). Voor meer operationele aspecten, zoals afstemming van vraag en aanbod van stikstof gedurende het groeiseizoen, zijn ook berekeningen op perceelsniveau nodig met actuele weersgegevens. In de periode 2003-2004 is in opdracht van HPA een perceelsversie ontwikkeld en getoetst op praktijkbedrijven.
    Multifunctionele mini-pc in borstzak
    Kingmans, R. - \ 2005
    Boerderij/Veehouderij 90 (2005)9. - p. 22 - 23.
    rundveehouderij - melkvee - automatisering - prestatieregistratie - registreren - informatiesystemen - computers - informatieopslag - agrarische bedrijfsvoering - cattle husbandry - dairy cattle - automation - performance recording - recording - information systems - computers - information storage - farm management
    Melkveehouder heeft een palmtop waarmee alle ingetypte waarnemingen in een keer in de computer worden opgeslagen. Dat spaart tijd en levert betrouwbare data
    Vroege besmetting vroeg bestrijden
    Wander, J.G.N. - \ 2005
    Boerderij/Akkerbouw 90 (2005)10. - ISSN 0169-0116 - p. 18 - 19.
    allium cepa - uien - gewasbescherming - ziektebestrijding - spuiten - peronospora farinosa - computers - informatiesystemen - toepassingsdatum - ziektepreventie - beslissingsondersteunende systemen - onions - plant protection - disease control - spraying - information systems - application date - disease prevention - decision support systems
    Wanneer in een uiengewas de eerste verschijnselen van valse meeldauw zijn te zien, is de infectie al zo'n 2 weken achter de rug. De computer helpt het juiste spuitmoment te bepalen
    In silico sampling reveals the effect of clustering and shows that the log-normal rank abundance curve is an artefact
    Neuteboom, J.H. ; Struik, P.C. - \ 2005
    NJAS Wageningen Journal of Life Sciences 53 (2005)2. - ISSN 1573-5214 - p. 223 - 245.
    gegevensverwerking - computers - gegevensanalyse - statistiek - grafieken - populatiedynamica - populatie-ecologie - data processing - computers - data analysis - statistics - graphs - population dynamics - population ecology - species-area - canonical distribution - diversity - patterns - commonness - rarity
    The impact of clustering on rank abundance, species-individual (S-N)and species-area curves was investigated using a computer programme for in silico sampling. In a rank abundance curve the abundances of species are plotted on log-scale against species sequence. In an S-N curve the number of species (S) is plotted against the log of the total number of individuals (N) in the sample, in a species-area curve S is plotted against log-area. The results from in silico sampling confirm the general shape of S-N and speciesarea curves for communities with clustering, i.e., a curve that starts with a smaller slope but that later is temporarily steeper than the curve expected for Poisson-distributed species. Extrapolation of S-N and species-area curves could therefore be misleading. The output furthermore shows that sigmoid rank abundance curves (curves of the type of a log-normal or broken stick) can be an artefact of the standard procedure of first sorting the species in sequence of abundance in combination with clustering in the low abundant and rare species. This makes the usual explanation given to the log-normal rank abundance curve dubious. An extension of the negative-binomial rank abundance curve-fit model is discussed to make it suitable for also fitting sigmoid rank abundance curves.
    Fax in de strijd tegen vruchtrot
    Wander, J.G.N. - \ 2005
    Groenten en Fruit. Algemeen (2005)21. - ISSN 0925-9694 - p. 35 - 35.
    aardbeien - teelt - gewasbescherming - botrytis - ziektebestrijding - fungiciden - spuiten - toepassingsdatum - adviescentra - informatiediensten - informatiesystemen - computers - telefoons - telecommunicatie - vollegrondsteelt - strawberries - cultivation - plant protection - botrytis - disease control - fungicides - spraying - application date - advisory centres - information services - information systems - computers - telephones - telecommunications - outdoor cropping
    Als aardbeien bloeien, ligt vruchtrot door Botrytis op de loer. Bij gunstige omstandigheden kan een onbeschermd gewas flinke aantasting oplopen. Dat leidt tot productieverlies, infectiebronnen en overbodig werk, want rotte vruchten moeten ook geplukt worden. De waarschuwingsfax houdt telers alert om tijdig te bestrijden
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