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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Een professionele schapenhouderij door efficiënter en slimmer gebruik van informatie : Kernpunten uit een inventarisatie in het veld
Holster, H.C. ; Antonis, A.F.G. ; Bergevoet, R.H.M. ; Vellema, P. ; Verkaik, J. ; Bokma-Bakker, M.H. - \ 2014
Wageningen UR
schapenhouderij - professionaliteit - professionele erkenning - kwaliteitszorg - bedrijfsinformatiesystemen - datacommunicatie - toekomst - sheep farming - professionalism - professional recognition - quality management - management information systems - data communication - future
In de periode 2013-2016 werken bedrijfsleven en schapenhouders (de sector) samen aan de uitdaging de schapenhouderij verder te professionaliseren. Hierbij is het economisch perspectief, met behoud van het goede imago, het uitgangspunt. Deze brochure bevat de populaire samenvatting van een verkennend onderzoek naar kansen voor verbinden en analyseren van datastromen in de schapenhouderij. Hierin stonden de volgende kennisvragen centraal : - Wat vindt de sector? - Welke datasystemen zijn er binnen de schapenhouderij? - Hoe ziet een gewenst toekomstbeeld er uit? - Op welke wijze kan het gewenste toekomstbeeld worden gerealiseerd?
Infrastructuur satellietdatabank
Lokers, R.M. ; Gijzen, S.W.J.G.M. - \ 2013
Wageningen : Alterra, Wageningen-UR - 4
precisielandbouw - geografische informatiesystemen - satellietbeelden - satellietkarteringen - computer software - datacommunicatie - gegevens verzamelen - gegevensbeheer - precision agriculture - geographical information systems - satellite imagery - satellite surveys - data communication - data collection - data management
Doelstelling is het ontwikkelen van een infrastructuur voor het ontsluiten van datasets afgeleid van de ruwe basisdata zoals beschikbaar is via de Nationale Satelliet databank. Ontsluiting vindt plaats volgens een Service Oriented Architecture (SOA) via de geëigende open standaarden en protocollen voor ontsluiting van ruimtelijke data, aansluitend op de principes en standaarden van OpenGIS en INSPIRE.
Pacioli 20: Complex farms and sustainability in farm level data collection
Vrolijk, H.C.J. - \ 2013
The Hague : LEI, onderdeel van Wageningen UR (LEI proceedings : Onderzoeksveld Agriculture & entrepreneurship ) - ISBN 9789086156344 - 239
agrarische economie - boekhouding van landbouwbedrijf - european farm accounting network - statistiek - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
For the 20th time, LEI organised the yearly Pacioli workshop. This year it took place in Rome, Italy, from 30 September to 3 October 2012. There were a record number of 48 participants from EU countries, non-EU countries such as Switzerland and Norway, candidate countries and from international organisations such as OECD, USDA, FAO and the European Commission. They discussed innovations and developments in the collection and use of farm level data. Important topics were the measurement of sustainability indicators, the specific problems of collecting information on large complex farms and the use of data for policy analysis and research. The Italian research institute INEA hosted the meeting and took care of the local organisation. LEI was responsible for organising the content of the programme and chairing the meetings.
Gegevens delen via Linked Open Data ; case study over het delen van grondwatergegevens bij de bouw van de A2 tunnel in Maastricht
Verhelst, E.C.H. ; Houtkamp, J.M. ; Randen, Y. van - \ 2012
Wageningen : Alterra (Alterra-rapport 2306) - 32
infrastructuur - wegen - tunnels - grondwaterstand - datacommunicatie - gegevensverwerking - zuid-limburg - infrastructure - roads - groundwater level - data communication - data processing
In dit rapport is een case study beschreven waarin wordt gekeken naar het delen van gegevens bij de bouw van een groot infrastructuur project (Maastricht A2). De manier van gegevensdelen die is uitgewerkt wordt Linked Open Data genoemd. Bij Linked Open Data zijn de brongegevens toegankelijk en aan elkaar verbonden met web links. Omdat de gegevens toegankelijk zijn via de bron kan elke partij zijn eigen overzichten maken en applicaties en visualisaties bouwen. De gekoppelde data vormen een wereldwijde netwerkstructuur waaraan makkelijk nieuwe gegevens kunnen worden toegevoegd. Zo wordt de samenhang tussen gegevens beter zichtbaar.
Pacioli 19; The role of FADN after the CAP reform
Vrolijk, H.C.J. - \ 2012
The Hague : LEI, part of Wageningen UR (LEI Memorandum / LEI Wageningen UR : Agriculture & entrepreneurship ) - ISBN 9789086155729 - 186
agrarische economie - boekhouding van landbouwbedrijf - statistiek - european farm accounting network - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
The international Pacioli network shares knowledge on the management and use of agricultural microeconomic databases (such as the Farm Accountancy Data Network in Europe). Each year LEI, part of Wageningen UR, organizes a Pacioli workshop in close cooperation with a local organizer. The 19th Pacioli workshop took place in Tallinn, Estonia in October 2011
Ontology spectrum for geological data interoperability
Ma, X. - \ 2011
University of Twente. Promotor(en): M. Molenaar, co-promotor(en): M.J. Kraak; P.J.M. van Oosterom; Arnold Bregt. - [S.l.] : S.n. - ISBN 9789061643234 - 184
geologie - datacommunicatie - gegevensbeheer - gegevensstructuren - gegevensanalyse - ontologieën - geology - data communication - data management - data structures - data analysis - ontologies
Standaardisatie van keteninformatie
Verdouw, C.N. - \ 2011
Agro Informatica 24 (2011)1. - ISSN 0925-4455 - p. 6 - 7.
agro-industriële ketens - ketenmanagement - informatiesystemen - datacommunicatie - standaardisering - agro-industrial chains - supply chain management - information systems - data communication - standardization
Het kunnen beschikken over de juiste, complete informatie op het juiste moment is de basis voor optimale ketensamenwerking. Een snelle, foutloze en efficiënte informatieoverdracht is alleen mogelijk als de informatiesystemen in een keten precies dezelfde taal spreken. Daarvoor moeten data uit het informatiesysteem van de zender automatisch ingelezen kunnen worden door het systeem van de ontvanger en de interpretatie van deze data moet in beide systemen gelijk zijn. Op bedrijfsprocessen gebaseerde informatiestandaarden zorgen daarvoor. Het zijn vaste afspraken over het formaat, de inhoud en de betekenis van de uit te wisselen informatie èn de manier, waarop deze technisch gecommuniceerd moeten worden.
AgriXchange: harmonisatie van data-uitwisseling in de Europese agri-food sector
Lokers, R.M. ; Verdouw, C.N. - \ 2011
Agro Informatica 24 (2011)1. - ISSN 0925-4455 - p. 21 - 22.
voedselketens - agro-industriële ketens - datacommunicatie - standaardisering - netwerken - informatieverspreiding - europa - food chains - agro-industrial chains - data communication - standardization - networks - diffusion of information - europe
Toegevoegde waarde PPO nog beter communiceren : interview Bert Pinxterhuis
Wildenbeest, G. ; Pinxterhuis, E.K. - \ 2011
BloembollenVisie 2011 (2011)210. - ISSN 1571-5558 - p. 12 - 13.
onderzoeksinstituten - toegevoegde waarde - bloembollen - datacommunicatie - landbouwkundig onderzoek - research institutes - value added - ornamental bulbs - data communication - agricultural research
Het collectief gefinancierde onderzoek van het PPO levert de bollensector een rendement op waar menige investeringsmaatschappij jaloers op zou zijn, 'zegt Bert Pinxterhuis, sinds 15 juni business unit manager - van PPO Bollen Bomen en Fruit te Lisse. Onderzoek naar bodemleven, teeltsystemen, fytosanitaire problemen en energie beschouwt hij als de grote onderzoeksthema's van de komende jaren.
Pacioli 18; Proceedings of the 18th international workshop on micro-economic databases in agriculture
Boone, J.A. ; Teeuwen, J.L. - \ 2010
The Hague : LEI, part of Wageningen UR (Report / LEI : Research area Agriculture & entrepreneurship ) - ISBN 9789086154623
agrarische economie - boekhouding van landbouwbedrijf - statistiek - european farm accounting network - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
The international Pacioli network shares knowledge on the management and use of agricultural micro-economic databases (such as Farm Accountancy Data Networks). Each year a workshop is organised by LEI, part of Wageningen UR, in close collaboration with a local organiser. The Pacioli 18 workshop took place in Ghent, Belgium, in September 2010.
Assessing spatial data infrastructures
Grus, L. - \ 2010
University. Promotor(en): Arnold Bregt, co-promotor(en): J. Crompvoets. - [S.l. : S.n. - ISBN 9789085856184 - 171 p.
infrastructuur - gegevensanalyse - geografische informatiesystemen - datacommunicatie - beoordeling - geoinformatie - ruimtelijke databases - infrastructure - data analysis - geographical information systems - data communication - assessment - geoinformation - spatial databases
Over the last two decades many countries and regions throughout the world have taken steps to establish Spatial Data Infrastructures (SDIs). Developing SDIs requires a considerable amount of time, energy and financial resources. Therefore it is increasingly important to assess SDI outcomes in order to justify the resources spent on those infrastructures. The main objective of this thesis is to develop a framework for assessing Spatial Data Infrastructures. This thesis achieves this main objective in four sub objectives. First, for the reason that SDI complexity is seen as a serious obstacle for its comprehensive assessment, this thesis analyses SDI complexity by determining whether SDI can be viewed as Complex Adaptive System (CAS). Second, the principles of assessing CAS and the norms of general evaluation theory serve as the basis for developing a Multi-view SDI assessment framework. Third, the thesis evaluates the application process and applicability of the Multi-view SDI assessment framework to assess SDIs by applying it in 21 National SDIs. Fourth, the thesis expands the Multi-view SDI assessment framework by adding an assessment view for a goal-oriented SDI assessment. The thesis results show that SDI can be viewed as Complex Adaptive System (CAS). The principles of assessing CAS serve as a basis for developing a Multi-view SDI assessment framework which allows for a more comprehensive and less biased SDI assessment. The evaluation of the Multi-view SDI assessment framework in 21 National SDIs demonstrates it potential to assess SDIs. This thesis also expands the Multi-view SDI assessment framework by adding an assessment view for a goal-oriented SDI assessment. The developed assessment view is tested by applying it to measure the goals realization of the Dutch SDI.
PACIOLI 17; Innovation in the management and use of Micro Economic Databases in Agriculture
Boone, J.A. ; Teeuwen, C. - \ 2009
Den Haag : LEI Wageningen UR (Report / LEI : Research area 2, Sectors and enterprises ) - ISBN 9789086153718 - 216
agrarische economie - boekhouding van landbouwbedrijf - statistiek - european farm accounting network - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
The PACIOLI network explores the need for and feasibility of innovation in farm accounting and its consequences for data gathering for policy analysis in Farm Accountancy Data Networks (FADNs). PACIOLI 17 took place in Ettenhausen, Switzerland, in June 2009. The theme of the workshop was 'Innovation in the management and use of Micro Economic Databases in Agriculture'.
Web services for transcriptomics
Neerincx, P. - \ 2009
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 - molecular biology - data communication - data processing - computer networks - 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
Workshop sensing a changing world : proceedings workshop November 19-21, 2008
Kooistra, L. ; Ligtenberg, A. - \ 2008
Wageningen : Centre for Geo-information, Wageningen University and Research Centre (CGI report CGI-08-005) - 123
sensors - globale plaatsbepalingssystemen - datacommunicatie - technologie - remote sensing - visualisatie - global positioning systems - data communication - technology - visualization
PCC Platform Communicatie on Climate Change
Dorland, R. van; Steenis, O.M.B. van - \ 2008
klimaatverandering - datacommunicatie - communicatie - toegepast onderzoek - interdisciplinair onderzoek - organisatie van onderzoek - milieucommunicatie - climatic change - data communication - communication - applied research - interdisciplinary research - organization of research - environmental communication
Poster informing about the Platform Communication on Climate Change, PCCC. PCCC was established by the Dutch climate research community to improve the quality, efficiency and effectiveness of the communication of Dutch climate research
IST 2006 event in Helsinki: strategies for leadership
Wolfert, J. - \ 2006
Agro Informatica 19 (2006)4. - ISSN 0925-4455 - p. 27 - 28.
informatietechnologie - landbouw - voeding - voedingsinformatie - projecten - datacommunicatie - conferenties - finland - netwerken - kennisoverdracht - information technology - agriculture - nutrition - nutrition information - projects - data communication - conferences - networks - knowledge transfer
Impressies van de IST 2006 (Information Society Technologies) in Helsinki met o.a. een presentatie van een aantal living labs
Relevante processen voor SALDO in beeld : State of the Art, een quick scan van de omgeving
Holster, H.C. ; Meulen, H.A.B. van der; Annevelink, E. ; Geerling-Eiff, F.A. ; Paassen, R.A.F. van; Schreuder, R. - \ 2006
Den Haag [etc.] : LEI [etc.] - 57
agrarische economie - overheidsbeleid - landbouwsector - informatietechnologie - datacommunicatie - boekhouding - agricultural economics - government policy - agricultural sector - information technology - data communication - accounting
Pacioli 11; New roads for farm accounting and FADN
Poppe, K.J. - \ 2004
Den Haag : LEI (Report / LEI : Domain 8, Models and data ) - ISBN 9052428786 - 168
agrarische bedrijfsvoering - european farm accounting network - boekhouding van landbouwbedrijf - gezinsinkomen - inkomsten uit het landbouwbedrijf - monitoring - europa - datacommunicatie - europese unie - farm management - farm accounting - household income - farm income - europe - data communication - european union
The Pacioli network explores the needs for and feasibility of innovation in farm accounting and its consequences for data gathering for policy analysis in Farm Accountancy Data Networks (FADNs). PACIOLI-11 was held in Przysick (Poland), in October 2003. This workshop report presents the papers. In the 11th Pacioli workshop special attention was given to a number household income issues, using micro data. Other topics include the CAP-Mid Term Review, farm specialisation, software development, and productivity analysis. In addition results of the workgroup sessions are reported.
Ondernemer centraal bij terugdringing administratieve lasten in Agrarisch Nederland; Verkenning naar de toekomstige informatie architectuur tussen overheid en agrarische ondernemingen
Annevelink, E. ; Geerling-Eiff, F.A. ; Kroeze, G.H. ; Meulen, H.A.B. van der; Stormink, H. ; Holster, H.C. ; Poppe, K.J. ; Schreuder, R. ; Paassen, R.A. van - \ 2004
Den Haag : LEI (Rapport / LEI : Domein 6, Beleid ) - ISBN 9052428883 - 92
agrarische economie - overheidsbeleid - landbouwsector - boekhouding van landbouwbedrijf - informatietechnologie - datacommunicatie - boekhouden - wetgeving - regelingen - nederland - agricultural economics - government policy - agricultural sector - farm accounting - information technology - data communication - book-keeping - legislation - regulations - netherlands
De Nederlandse regering heeft zich tot doel gesteld de administratieve lasten van ondernemersdrastisch te verlagen. Eén van de middelen daarbij is het beter gebruik maken vaninformatica- en communicatietechnologie, en het daarmee beter aansluiten op de bedrijfsprocessenvan ondernemingen. In opdracht van het Ministerie van LNV heeft een groeponderzoekers van Wageningen UR nagegaan of en hoe het centraal stellen van de ondernemerbij kan dragen aan de vermindering van administratieve lasten. Dit rapport beschrijftin een essay en negen wetenschappelijke hoofdstukken welke mogelijkheden en valkuilener zijn. Gepleit wordt voor een publiek-private samenwerking rond dit thema.
W-learning voor Geo-informatie
Boxel, P. van; Wentzel, P. ; Lammeren, R.J.A. van; Boschma, S. ; Molendijk, M. ; Bruin, S. de - \ 2004
Amsterdam : Vrije Universiteit (GISPY-rapport 2004-11) - 17
onderwijs - geografie - leeractiviteiten - onderwijsvernieuwing - mobiele uitrusting - draagbare instrumenten - telecommunicatie - datacommunicatie - education - geography - learning activities - educational innovation - mobile equipment - portable instruments - telecommunications - data communication
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