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Advancement of farming by facilitating collaboration : reference architectures and models for farm software ecosystems
Kruize, Jan Willem - \ 2017
University. Promotor(en): Adrie Beulens, co-promotor(en): Huub Scholten; Sjaak Wolfert. - Wageningen : Wageningen University - ISBN 9789462579668 - 242
farming - information technology - computer software - farms - models - farm management - information systems - landbouw bedrijven - informatietechnologie - landbouwbedrijven - modellen - agrarische bedrijfsvoering - informatiesystemen

Since time began, mankind has been threatened by the combination of growing populations and diminishing resources. Present-day, this threat is very pertinent as mankind is challenged by a growing world population that is expected to exceed 10 billion in 2050, while resources diminish. Simultaneously, increase of food production should be accomplished in a sustainable manner as consumers require food to be produced environmentally-friendly. Moreover, consumers require safe food produced in transparent agri-food supply chain networks. Farm enterprises can contribute by advancing their management to increase food production in a sustainable, safe and transparent manner. A well-known advanced farm management style, which is knowledge and information intensive, is precision agriculture. Precision agriculture increases the profitability of crop production, while simultaneously reducing the negative environmental impact by tight monitoring and control, in which applications rates of agricultural inputs are adjusted to local needs. Such advanced farm management requires integrated farm information systems as it is knowledge and information intensive. However, advancement is hindered because of interoperability issues between software systems of multiple vendors. An integrated farm information system, containing components of multiple vendors, is required as single organisations cannot develop all technical solutions and ICT Components (e.g. tractors, implements, FMIS, decision support tools) that farmers require. A global overarching system, developed by a single vendor, that can support all business functions of farmers is therefore neither a feasible nor, from a competitive point of view, a desirable solution in agriculture. To realize farm enterprise integration we combine the approaches ICT Mass Customisation with Best-of-Breed. ICT mass customisation combines advantages of standard and customised software by enabling on-demand configuration of information systems from standard components with standardised interfaces. These ICT components can be supplied by different software vendors, which allow Best-of-Breed solutions. By realization of these approaches farm enterprise integration can improve. A farm enterprise can be an arable farm, livestock farm or horticultural farm. In this thesis we focus on arable farm enterprises.

To enable farm enterprise integration we have developed six artefacts that are presented in this thesis which are:

The Reference Architecture of Agricultural Enterprises (RAAgE) 1.0 that can describe farm enterprise architectures in a uniform and efficient manner;

A problem description, which is a case specific instantiation of RAAgE 1.0 generalized to a generic problem description;

An ontology that supports communication between collaborating actors and components;

Reference Architecture for Farm Software Ecosystems that defines generic relationships between actors and components;

RAAgE 2.0 that is a technical reference model to support configuration of business processes and ICT components, which is based on RAAgE 1.0;

Prototype software that serves as a proof of concept substantiating that all previous components will provide a solution for integration problems at farm enterprises.

RAAgE 1.0 supports designing enterprise architectures in a uniform and efficient manner. The reference model is described in a standard modelling language, named ArchiMate, and shows the interrelations between the business, application and technology layers of farm enterprises. The reference model includes an ontology to provide a concise and precise, formal specification of the object system. This is required to have a shared understanding and effective communication between researchers, farmers, software developers and other stakeholders involved. This ontology is used and extended in other parts of our research. The architectural descriptions can depict the relations between farm business processes and the ICT Components used. The model is validated by two experts that have experience in developing reference architectures and models.

A detailed problem description is created using RAAgE 1.0 to gain insight in the cause and nature of integration problems at farm enterprises. To find these problems a method was developed and applied in a case study research including three arable farm enterprises producing potatoes. These farm enterprises focused on improving their management and invested in new technologies for innovation. Within multiple steps of the method the architectural descriptions developed with RAAgE 1.0 facilitated communication and provided insight into problems of farm enterprises to achieve more advanced farm management. The case specific problems, described by instantiating RAAgE 1.0, have been analysed and formulated as more generic problems for farm enterprise integration. These generic problem descriptions have been validated with national and international experts. Based on this research we found that the cause and nature of current integration problems in farming are that ICT components used within the same farm enterprise:

have partly overlapping and partly unique application services, functions and interfaces (that are non-standard);

are missing required application services, functions and interfaces,

have disjoint data repositories;

have inadequate and incomplete data exchange as semantics are not unambiguously defined;

are hard to configure while this configuration is not supported by an actors and tools.

A design, addressing these problems is expected to solve current integration bottlenecks. First, this design must enable smooth data handling and seamless data exchange between ICT Components to solve inadequate and incomplete data exchange and enable integration of data repositories of multiple vendors. Second, it must include a configuration approach to link ICT Components to each other in a meaningful and coherent way. This should be supported by actors that are willing to configure ICT Component of multiple vendors into an integrated solution. Third, the design must enable the formation of a software enterprise to address the previous points and to organize collaboration between actors involved. This software enterprise should focus both on improving interoperability to contribute in solving problems with partly overlapping and partly unique application services, functions and interfaces as well as on organizing the development of missing application services, functions and interfaces.

To address these integration challenges a Reference Architecture for Farm Software Ecosystems and RAAgE 2.0 were developed, focusing on both technical and organizational aspects.

From literature we found that collaboration can take place within Software Ecosystems. Software Ecosystems are defined as the interaction of a set of actors on top of a common technological platform that results in a coherent set of ICT components or Services. They can provide an effective way to construct large software systems on top of a software platform by combining components, developed by actors that are part of different organisations. To support instantiation of Software Ecosystems for farming, a Reference Architecture was developed. This Reference Architecture describes how software developers, farmers and other stakeholders can collaborate to enable development, configuration and instantiation of integrated software solutions. More specifically, it can be used to map, assess, design and implement Farm Software Ecosystems to help to decrease current integration problems. The reference architecture comprises five main components:

Actors, which are basically app developers, business architects/software developers and end-users, i.e. farmers that finally use the configured ICT components and services;

Platform that enables configuration of Atomic Application Components into integrated information systems for farmers;

Open software enterprise that manages the relation between the actors and the platform;

Business services that support software configuration, development and hosting;

ICT Components that are configured application components from multiple vendors allowing seamless data exchange based on standards

After the design the reference architecture was first verified based on the requirements. Second, semi-structured interviews were held with experts to validate the model. Moreover, the assessment and mapping functionally was validated by using the reference architecture in a case study, in which two existing farm software ecosystems were assessed and mapped.

The Reference Architecture for Farm Software Ecosystems mainly addresses the organizational part of this research question. The technical part on the configuration of different ICT components into integrated solutions was not yet sufficiently covered in the Reference Architecture for Farm Software Ecosystems. Therefore we designed RAAgE 2.0 to improve the integrating capabilities of ICT Components, focussing on configuration and ICT Mass Customisation. In this research RAAgE 1.0 was extended into RAAgE 2.0 supporting technical aspects related to configuration of ICT Components by providing a hierarchical configuration methodology. This methodology divides configuration in two steps (i) business process configuration and (ii) software configuration. To enable business process configuration the model comprises three reference models, i.e. on products, processes and resources. The dependencies between these models are defined in rules that define possible combinations of products, processes and resources and that constrain the configuration of farm-specific models i.e. instances. The reference model also includes a configuration tree and templates. Templates describe a set of pre-configured product, process and resource models for typical cases. Variety in farm business processes can be modelled with business process variants. Such a variant realizes a similar kind of business services (e.g. basic fertilization, precision fertilization). Each variant has partly overlapping business processes and resources and unique ones. RAAgE 2.0 provides insight into these specific and generic parts. The other part of the methodology, software configuration, is divided in two additional sub-steps. The first sub-step is to create configuration templates that describe the required (generic) application services (capability types) to support specific business process variants. These configuration templates describe the interactions between the capability types. This sub step is typically performed by a business architect in close collaboration with software developers. The second sub-step is the selection and configuration of the specific capability of a capability type. Capabilities can be offered by atomic application components of multiple vendors that need to be selected. This second sub-step is performed by a business architect, in close collaboration with a farmer. With this extension RAAgE 2.0 supports (i) development of ICT components that fit within an ICT Mass Customisation and Best-of-Breed approach, (ii) selection of ICT components based on business processes that they should support and (iii) getting insight into configuration of different ICT components into an integrated farm information system.

To substantiate that our artefacts contribute to realizing ICT Mass Customisation in combination with Best-of-Breed in arable agriculture a proof of concept was developed. A proof of concept is defined as a phase in development, in which experimental hardware or software is constructed and tested to explore and demonstrate the feasibility of a new concept. Realizing ICT Mass Customisation requires: (i) software modularity, (ii) an information integration platform, (iii) component availability, (iv) configuration support and (v) reference information models. To fulfil these requirements a design was developed and instantiated for a specific use case on late blight protection in potato growing for a specific farmer in The Netherlands. For that purpose we:

configured the business processes that are involved in late blight protection using RAAgE 2.0 to identify which advanced ICT components are needed to support this process for this farmer;

developed the required advanced ICT components that were identified in the previous step using the FIspace platform. These components were provided by different app developers from 5 different European countries;

configured a composite application component within the FIspace platform using the configuration framework of RAAgE 2.0. This included involvement of 5 different European organizations;

instantiated and executed the application component within the FIspace platform for this specific farmer.

This resulted in prototype software that showed how we can configure business processes and multi-vendor atomic application components into a composite component to support late blight protection in potatoes for a specific farmer. It was made plausible that this approach is also applicable to other cases to create software able to support other business processes in agriculture.

Within this research we developed artefacts and substantiated that they facilitate collaboration between the actors involved and can help to develop ICT Components that improve farm enterprise integration. Still, to make ICT Mass Customisation and Best-of-Breed a more common practice, future research is required. In this research we recommend to focus on:

Development of business models to gain insight into the motives of software developers to become part of Farm Software Ecosystems. Insight into these motives can enhance the adoption of Software Ecosystems for agriculture, which makes the concept of ICT Mass Customisation more feasible.

Improving configuration of atomic application components and supporting tools as this is currently still cumbersome. We recommend focussing on one specific case to dig into all details of the case. Such a detailed description will be re-usable for many other farm business processes such as fertilization, other types of crop protection, seeding and harvesting.

Although, there are still hurdles to take we recommend continuing this research line as it can result in improved farm enterprise integration and adoption of advanced farm management styles by famers. This can enable farm enterprises to increase food production, while producing in a sustainable, safe and transparent manner.

Goed registreren, welk systeem?
Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, J.K. - \ 2016
Zeldzaam huisdier 41 (2016)4. - ISSN 0929-905X - p. 10 - 11.
zeldzame rassen - dieridentificatiesystemen - informatiesystemen - gegevens verzamelen - registreren - stamboeken - rare breeds - animal identification systems - information systems - data collection - recording - herdbooks
In voorgaande edities van
Zeldzaam Huisdier is aandacht
gegeven aan verschillende systemen
voor het registreren van
(zeldzame) rassen, te weten:
Zoo Easy, Iris, GReIS en Elda,
Falcoo en Equis (Delta Horses).
In dit laatste artikel van deze
reeks geven we een overzicht
van deze systemen.
Cybersecurity in the Agrifood sector
Bogaardt, M.J. ; Poppe, K.J. ; Viool, V. ; Zuidam, E. van - \ 2016
Capgemini Consulting - 8 p.
food production - agricultural production - data management - information systems - computer sciences - safety - crime - voedselproductie - landbouwproductie - gegevensbeheer - informatiesystemen - computerwetenschappen - veiligheid - misdaad
Every day new digital applications find their way into our lives. Digitization has brought our society many benefits and will do so for the coming years as key enabler for our economy. It is an important driver behind innovation and economic growth. However, to create sustainable innovation and frequent use, security is absolutely essential. Due to the increased frequency of high tech possibi¬lities, the chance of technical failure or severe misusage and abuse of vulnerabilities can become a realistic threat. This article deals with cybersecurity in the agrifood sector.
Plan for collaborative working with ROC+
Vogels, J.W.P.M. ; Hamersveld, N. - \ 2015
Wageningen : Wageningen UR - Food & Biobased Research (Report / Food & Biobased Research 1588) - 11
data management - ontologies - computer software - information systems - cooperation - user interfaces - gegevensbeheer - ontologieën - informatiesystemen - samenwerking - gebruikersinterfaces
OM 2.0
Rijgersberg, H. ; Wigham, M.L.I. ; Willems, D.J.M. ; Top, J.L. - \ 2015
Wageningen : Wageningen UR - Food & Biobased Research (Report / Wageningen UR Food & Biobased Research 1596) - ISBN 9789462575264 - 9
ontologieën - eenheden - meting - gegevensbeheer - computer software - informatiesystemen - ontologies - units - measurement - data management - information systems
ROC+ as a consultancy service
Luijendijk, L. ; Wigham, M.L.I. - \ 2015
Wageningen : Wageningen UR - Food & Biobased Research (Report / Wageningen UR Food & Biobased Research 1589) - ISBN 9789462575226 - 10
gegevensbeheer - ontologieën - computer software - informatiesystemen - consultancy - kennisoverdracht - data management - ontologies - information systems - knowledge transfer
Rosanne: islands of structure in unstructured data : final report 2015 : Rosanne valorisation project
Wigham, M.L.I. ; Rijgersberg, H. ; Timmer, M.J. ; Top, J.L. - \ 2015
Wageningen : Wageningen UR - Food & Biobased Research (Report / Wageningen UR Food & Biobased Research 1590) - ISBN 9789462575233 - 14
gegevensbeheer - computer software - informatiesystemen - informatieontsluiting - logica - ontologieën - toepassingen - data management - information systems - information retrieval - logic - ontologies - applications
Bodem in beweging: BIS Nederland informeert
Knotters, M. ; Okx, J.P. ; Hack-ten Broeke, M.J.D. ; Vries, F. de - \ 2015
Bodem 25 (2015)3. - ISSN 0925-1650 - p. 11 - 13.
bodemkarteringen - bodemwater - bodemfysica - bodem - informatiesystemen - soil surveys - soil water - soil physics - soil - information systems
Bodemkundig InformatieSysteem informeert over actuele toestand èn dynamiek. De bodem die we kennen vanaf het eerste moment dat we een bodemkaart zagen, lijkt onveranderlijk. Maar kijken we wat beter naar de bodem zelf, zoals bodemkundigen dat doen, dan zien we volop beweging
Bodemfysische gegevens in BIS
Bakker, G. ; Heinen, M. ; Wesseling, J.G. ; Groot, W.J.M. de; Assinck, F.B.T. ; Hummelink, E.W.J. - \ 2015
Wageningen : Alterra (Alterra-rapport 2613)
bodemfysica - bodemwater - organische stof - informatiesystemen - soil physics - soil water - organic matter - information systems
Bodemfysische gegevens, zoals de waterretentiekarakteristiek en doorlatendheidskarakteristiek, organisch stofgehalte, textuurgegevens, profielbeschrijving en andere metagegevens zijn belangrijke basisgegevens bij het modelleren van transport van water en opgeloste stoffen in de onverzadigde zone, maar vinden ook tal van andere toepassingen. Omdat er grote behoefte is aan actuele bodemfysische gegevens van hoge kwaliteit en omdat de huidige databases onvoldoende opschalingsmogelijkheden bieden, zijn in dit project 100 nieuwe bodemfysische gegevens van goede kwaliteit gegenereerd. De bodemfysische gegevens en de bijbehorende beschrijvende gegevens zijn ondergebracht in het BIS (Bodem Informatie Systeem). Aanvullend is van 91 bestaande bodemfysische gegevens van hoge kwaliteit in Priapus een koppeling gelegd met beschrijvende gegevens in BIS en de literatuur, zodat er in totaal 191 bodemfysische monsters beschikbaar zijn.
Critical success factors for implementing supply chain information systems : insights from the pork industry
Denolf, J.M. - \ 2014
University. Promotor(en): Onno Omta; Jack van der Vorst, co-promotor(en): Jacques Trienekens. - Wageningen : Wageningen University - ISBN 9789462571594 - 177
operationeel onderzoek - ketenmanagement - informatiesystemen - varkens - vee- en vleesindustrie - operations research - supply chain management - information systems - pigs - meat and livestock industry

Critical success factors for implementing supply chain information systems – Janne M. Denolf

Due to intensified competition, companies realize that they should closely collaborate with their supply-chain partners to further cut costs and stay competitive. To do so, supply-chain partners should intensify information sharing, which is often facilitated through supply chain information systems (SCIS). Implementation of such a system is a complex undertaking due to the umpteen technical and organizational aspects that require consideration. Multiple theories have given valuable insights into the complex interplay of organization and technology. However, tangible tools that consider these theories for implementing a supply chain information system are scarce. To provide more ready-to-use methods, the main objective of the thesis is to identify organizational and technical critical success factors (CSFs) for sharing information and implementing supply chain information systems (SCISs). CSFs are the factors that must go well during an implementation and must, therefore, be given special and continual attention in order to successfully implement an information system. This central objective is investigated by means of the pork industry.

In Chapter 2, we pay particular attention to (supply chain) information sharing. The literature indicates that the relationships among the supply-chain partners have to be managed, and effective governance structures need to be chosen for effective and efficient information sharing. Despite initial research, the literature has not accounted for the multi-dimensionality of information sharing and does not consider the complete supply chain as the unit of analysis. This leads to the first research objective: to investigate how and to what extent supply chain information sharing can be explained by supply chain governance structures. To gain insights regarding the research objective, three European pork supply chains with different governance structures were investigated. Through cross-case analysis, the study stipulates that apart from governance structures, quality regulations, the financial strength (of one or more supply-chain partners) and relationship management seem to influence information sharing to a great extent.

As stated in Chapter 2, supply chains increasingly share information through implementing automated SCISs. To manage these implementations carefully, the study of CSFs for SCIS implementations forms a promising approach. Since to date no consensus has been reached on SCIS critical success factors, the second objective is to identify critical success factors for implementing SCISs. Based on 10 key articles focusing on ERP implementations, we have built a list of CSFs as a starting point for the SCIS literature search. Thereafter, based on 21 SCIS articles, 14 CSFs for supply-chain information system implementation have been defined. To indicate the nature of the CSFs and highlight the interaction of the organizational and technical system, the CSFs are classified in the MIT90s framework of Scott Morton (1991) (See Figure 1).

Figure 1. Framework of CSFs for SCIS implementations

Chapter 3 identifies a comprehensive framework of CSFs for implementing SCISs. Concrete guidance for applying CSFs has, however, not been provided by the CSF literature. There is a gap between the rather abstract CSFs for SCIS implementations and operational project management. Consequently, the following third objective is posed: to make critical success factors for implementing supply chain information systems “actionable”. To deal with this objective, we investigated the completed implementation of SCISs in four German pork supply chains. Respondents were asked to describe crucial challenges during the project and actions taken to cope with these challenges (i.e. Critical Incident Technique). Challenges were assigned to CSFs and form a basis upon which to take actions. Our results suggest that “convince future users to use the new SCIS” – part of the CSF “manage change and deliver training” – and “define the functional requirements of the SCIS” – part of the CSF “select standards, vendor, and software package” – are frequently mentioned challenges. Furthermore, possible critical actions – with connected supply-chain responsibilities – are identified for implementing a SCIS. All in all, through this research, we link the concepts CSFs, challenges, and actions and bridge the gap between CSFs and operational project management for the implementation of a SCIS.

The fourth research objective deals with traceability systems, which are specific SCISs, aiming at the collection, documentation, maintenance, and application of information related to all processes in the supply chain in a manner that provides guarantees to consumers and stakeholders on origin, location, and life-history of a product. Despite a number of traceability and RFID publications, these publications fall short as they often deal with the general issue of traceability and are not really applicable for practitioners. Identification of critical traceability points (CTPs), which are points where information regarding traceability may get lost, is a suitable method for making traceability research more applicable. At last, the following fourth research objective is posed: to identify CTPs in organic pork supply chains and to investigate how these CTPs can be managed through the application of RFID in these chains. Data were collected through an in-depth case study in the European organic pork industry. After having mapped the production processes and information flows for farm and slaughterhouse, CTPs were identified. To keep such information available for actors in the supply chain, pigs should be uniquely identified throughout the supply chain and transformations at farm and slaughterhouse recorded. In the supply chain investigated, 18 CTPs are identified. Then, it was verified how and to what extent CTPs could be managed using RFID applications. The results indicate that several CTPs can be managed using RFID, but additional organizational measures, and the use of other identification technologies, such as DNA profiling, are imperative to manage all CTPs. On top of that, a new SCIS should be built, coupling different existing computer systems of actors involved.

On a general level, this thesis makes a contribution to the theories examining and explaining the mutual interaction of organizational and technical aspects. Specifically, tangible tools are provided that consider these theories for implementing SCISs. Organizational and technical critical success factors – and connected actions – are identified and classified in the MIT90s framework, which is in line with the Structuration Theory of Orlikowski (1992) and reflects the project life cycle of Markus and Tanis (2000). Using the framework of 14 CSFs, a more ready-to-use method is provided for implementing SCIS. Specifically, the thesis makes contributions to the literature on critical success factors (CSF) and critical traceability points (CTP). First, by identifying critical success factors (CSFs) for implementing SCISs, the CSF literature base is extended. Moreover, through identification of key actions for the CSFs, this thesis responds to a stream of researchers claiming that CSFs are not “actionable”. Second, compared to previous research, we investigate how and to what extent critical traceability points can be managed using new technologies such as Radio Frequency Identification (RFID). By verifying best practices and applications for RFID deployment, we provide a response to a group of researchers who stated that RFID and traceability research are not really applicable for practitioners.

KWIN nu ook als app
Rotgers, G. ; Vermeij, I. - \ 2014
V-focus 11 (2014)5. - ISSN 1574-1575 - p. 37 - 37.
veehouderij - pluimveehouderij - varkenshouderij - rundveehouderij - informatiesystemen - statistische gegevens - kwantitatieve analyse - agrarische economie - bedrijfseconomie - begroting van agrarisch bedrijf - bedrijfsvergelijking in de landbouw - toepassingen - livestock farming - poultry farming - pig farming - cattle husbandry - information systems - statistical data - quantitative analysis - agricultural economics - business economics - farm budgeting - farm comparisons - applications
KWIN, Kwantitatieve Informatie Veehouderij, verscheen de afgelopen 25 jaar als lijvig handboek, zowel op papier als digitaal. Dit najaar is daar een serie apps bij gekomen, waarmee adviseurs en veehouders zelf saldo- en kostprijsberekeningen kunnen maken. De apps zijn beschikbaar voor de pluimvee-, varkens- en rundveehouderij.
The green information chain : Groen Kennisnet brings agricultural knowledge from research to the classroom, on the farm, and into agri-business
Genderen, R.A. van; Ringersma, J. - \ 2014
kennisoverdracht - informatieverspreiding - informatiesystemen - kennis - landbouw - tuinbouw - voeding - dierhouderij - natuur - knowledge transfer - diffusion of information - information systems - knowledge - agriculture - horticulture - nutrition - animal husbandry - nature
“Groen Kennisnet” creates a content collection and professional “green” knowledge base (agriculture, horticulture, animal welfare, environmental protection, water management, food, fisheries). “Groen Kennisnet” makes these available to the Dutch agricultural education system and agri-business, and organizes communities around specific themes. “Groen Kennisnet” thus contributes to the connection between innovation in research and business & teaching. In our paper we explain how we organize the green information chain, the IT infrastructure and the communities. The combination of content, IT and community results in bringing new innovative knowledge available in the classroom and on the farm.
The Farmer’s Perspective: Bridging the Last Mile to Market
Doorneweert, R.B. ; Bhan, N. ; Kumunya, W. ; Esko, S. - \ 2014
Den Haag : LEI Wageningen UR (LEI 14-006) - 25
landbouwontwikkeling - innovatie adoptie - duurzame ontwikkeling - aanpassingsvermogen - kenya - houding van boeren - sociale participatie - waardeketenanalyse - informatiesystemen - ontwikkelingssamenwerking - agricultural development - innovation adoption - sustainable development - adaptability - farmers' attitudes - social participation - value chain analysis - information systems - development cooperation
The Kenyan ‘farmer’ value chain was not just a neat box in the formal structure of a value chain, but a flexible, multipurpose node in the rural economy’s complex web of human interaction and exchange of goods, services and knowledge. Therefore we have called it the agricultural value web. This is the main conclusion from the inquiry on adoption of information and technology services with farmers in their rural communities. LEI Wageningen UR has executed this inquiry on behalf of the Dutch Ministries of Foreign Affairs and Economic Affairs.
Reactie op het artikel ‘Controle van kalibratiegegevens’
Knotters, M. ; Hoogland, T. - \ 2013
Stromingen : vakblad voor hydrologen 19 (2013)3/4. - ISSN 1382-6069 - p. 125 - 126.
hydrologie - grondwaterstand - watervoorziening - informatiesystemen - kalibratie - hydrology - groundwater level - water supply - information systems - calibration
Grondwaterstandsinformatie van goede kwaliteit vinden wij belangrijk. Iedere inspanning om deze kwaliteit vast te stellen en te verbeteren juichen wij toe, vooral als zo’n inspanning wetenschappelijk degelijk is onderbouwd. Wat betreft dat laatste willen wij graag twee opmerkingen plaatsen bij het artikel ‘Controle van kalibratiegegevens’ van Jaco van der Gaast in Stromingen 19(2), pag. 85-90
ICT in de Nederlandse sierteelt: Een analyse van de huidige situatie en uitdagingen voor de virtualisering van sierteeltnetwerken
Verdouw, C.N. ; Beulens, A.J.M. - \ 2013
Wageningen : Da Vinc3i (WP3 Virtuele informatie-uitwisseling en transparantie D3.3) - 77
tuinbouw - sierteelt - informatiesystemen - netwerken (activiteit) - informatiemanagement - procesoptimalisatie - ketenmanagement - virtuele realiteit - tracking en tracing - horticulture - ornamental horticulture - information systems - networking - information management - process optimization - supply chain management - virtual reality - tracking and tracing
Het DaVinc3i project onderzoekt hoe de Nederlandse sierteeltsector in het virtuele handelsnetwerk zijn leidende concurrentiepositie in wereldwijde sourcing en afzet van bloemen en planten in Europa kan versterken. Informatie- en communicatietechnologie (ICT) heeft een sleutelrol in de virtualisering van deze netwerken. Dit document geeft een overzicht van de huidige situatie en adresseert vervolgens uitdagingen voor het realiseren van virtuele l ogistieke netwerken in de Nederlandse sierteelt. Stand van Zaken ICT in sierteeltketens De analyse van de stand van zaken is gebaseerd op een inventarisatie die van eind 2011 tot begin 2012 is uitgevoerd en in oktober 2013 is geactualiseerd.
Agrimatie : informatie over de agrosector
Fernhout, C.Y. ; LEI, - \ 2013
Den Haag : LEI Wageningen UR
landbouwsector - statistiek - overheidsbeleid - prijzen - informatiesystemen - economische indicatoren - duurzaamheidsindicatoren - agricultural sector - statistics - government policy - prices - information systems - economic indicators - sustainability indicators
Deze website toont diverse onderzoeksresultaten die LEI Wageningen UR in het kader van Wettelijke onderzoekstaken publiceert voor het Ministerie van Economische Zaken.
De effecten van een open basisregistratie topografie (BRT)
Bregt, A.K. ; Castelein, W.T. ; Grus, L. ; Eertink, D. - \ 2013
Wageningen : Wageningen University - 41
landgebruik - topografie - informatiesystemen - kadasters - gebruik - maatschappelijke betrokkenheid - monitoring - land use - topography - information systems - cadastres - usage - community involvement
Op 1 januari 2012 is basisregistratie topografie (BRT) als open data aan de maatschappij ter beschikking gesteld. Deze stap zal zeer waarschijnlijk aanzienlijke effecten hebben op het gebruik van deze gegevens. Wat deze effecten zijn is echter onbekend. Om meer inzicht in deze effecten te krijgen is door de Wageningen Universiteit en het Kadaster en monitor ontwikkeld. Deze monitor richt zich, via indicatoren, op het meten van de effecten op de maatschappij (externe effecten), de interactie tussen het Kadaster en de maatschappij (relatie effecten) en het Kadaster (interne effecten).
Onderzoek naar de grondwaterstandsdynamiek in NHI v2.1 : hoofdrapport
Bakel, J. van; Pastoors, R. ; Massop, H.T.L. ; Hunink, J. ; Hoogewoud, J. ; Vergroesen, T. - \ 2012
NHI - 10
grondwaterstand - hydrologie - watersystemen - informatiesystemen - groundwater level - hydrology - water systems - information systems
Op 1 november 2010 is NHI versie 2.1 (Nationaal Hydrologisch Instrumentarium, versie 2.1) opgeleverd. In de rapportage is aangegeven dat de grondwaterstanden onvoldoende aansluiten bij de grondwaterstandsmetingen. Naast significante afwijkingen in het absolute niveau (GLG en GHG) vertonen de gesimuleerde grondwaterstanden in voor zoetwateraanvoer relevante gebieden te weinig dynamiek, mede volgens de regionale analyses die in 2010 door STOWA zijn gehouden (STOWA rapport 2011-06). Om dit nader te onderzoeken is door de NHI projectgroep een Task Force Grondwaterstandsdynamiek opgericht met specialisten van binnen en buiten NHI die als taak heeft om de grondwaterstandsdynamiek in NHI te analyseren en waar nodig en mogelijk voorstellen tot verbetering te doen.
sCore eindrapportage
Koenderink, N.J.J.P. ; Willems, D.J.M. ; Batenburg, R.A. van; Wigham, M.L.I. ; Malek, H.E. - \ 2012
Wageningen : Wageningen UR - Food & Biobased Research (Rapport / Wageningen UR Food & Biobased Research 1341) - 21
bedrijven - toepassingen - computertechnieken - consulenten - informatiesystemen - businesses - applications - computer techniques - consultants - information systems
In opdracht van Syntens heeft de Intelligent Systems groep van Wageningen UR Food & Biobased Research de sCore-applicatie gebouwd. De sCore-applicatie is een van de pijlers in het project “De Toekomst Bedrijven”. Dit is de eindrapportage van het sCore-project.
From existing data to novel hypotheses : design and application of structure-based Molecular Class Specific Information Systems
Kuipers, R.K.P. - \ 2012
University. Promotor(en): Vitor Martins dos Santos; G. Vriend, co-promotor(en): Peter Schaap. - S.l. : s.n. - ISBN 9789461733504 - 231
systeembiologie - bio-informatica - genomica - informatiesystemen - computerwetenschappen - databanken - datamining - eiwitten - eiwitexpressieanalyse - systems biology - bioinformatics - genomics - information systems - computer sciences - databases - data mining - proteins - proteomics

As the active component of many biological systems, proteins are of great interest to life scientists. Proteins are used in a large number of different applications such as the production of precursors and compounds, for bioremediation, as drug targets, to diagnose patients suffering from genetic disorders, etc. Many research projects have therefore focused on the characterization of proteins and on improving the understanding of the functional and mechanistic properties of proteins. Studies have examined folding mechanisms, reaction mechanisms, stability under stress, effects of mutations, etc. All these research projects have resulted in an enormous amount of available data in lots of different formats that are difficult to retrieve, combine, and use efficiently.

The main topic of this thesis is the 3DM platform that was developed to generate Molecular Class Specific Information Systems (3DM systems) for protein superfamilies. These superfamily systems can be used to collect and interlink heterogeneous data sets based on structure based multiple sequence alignments. 3DM systems can be used to integrate protein, structure, mutation, reaction, conservation, correlation, contact, and many other types of data. Data is visualized using websites, directly in protein structures using YASARA, and in literature using Utopia Documents. 3DM systems contain a number of modules that can be used to analyze superfamily characteristics namely Comulator for correlated mutation analyses, Mutator for mutation retrieval, and Validator for mutant pathogenicity prediction. To be able to determine the characteristics of subsets of proteins and to be able to compare the characteristics of different subsets a powerful filtering mechanism is available. 3DM systems can be used as a central knowledge base for projects in protein engineering, DNA diagnostics, and drug design.

The scientific and technical background of the 3DM platform is described in the first two chapters. Chapter 1 describes the scientific background, starting with an overview of the foundations of the 3DM platform. Alignment methods and tools for both structure and sequence alignments, and the techniques used in the 3DM modules are described in detail. Alternative methods are also described with the advantages and disadvantages of the various strategies. Chapter 2 contains a technical description of the implementation of the 3DM platform and the 3DM modules. A schematic overview of the database used to store the data is provided together with a description of the various tables and the steps required to create new 3DM systems. The techniques used in the Comulator, Mutator and Validator modules of the 3DM platforms are discussed in more detail.

Chapter 3 contains a concise overview of the 3DM platform, its capabilities, and the results of protein engineering projects using 3DM systems. Thirteen 3DM systems were generated for superfamilies such as the PEPM/ICL and Nuclear Receptors. These systems are available online for further examination. Protein engineering studies aimed at optimizing substrate specificity, enzyme activity, or thermostability were designed targeting proteins from these superfamilies. Preliminary results of drug design and DNA diagnostics projects are also included to highlight the diversity of projects 3DM systems can be applied to.

Project HOPE: a biomedical tool to predict the effect of a mutation on the structure of a protein is described in chapter 4. Project HOPE is developed at the Radboud University Nijmegen Medical Center under supervision of H. Venselaar. Project HOPE employs webservices to optimally reuse existing databases and computing facilities. After selection of a mutant in a protein, data is collected from various sources such as UniProt and PISA. A homology model is created to determine features such as contacts and side-chain accessibility directly in the structure. Using a decision tree, the available data is evaluated to predict the effects of the mutation on the protein.

Chapter 5 describes Comulator: the 3DM module for correlated mutation analyses. Two positions in an alignment correlate when they co-evolve, that is they mutate simultaneously or not at all. Comulator uses a statistical coupling algorithm to calculate correlated mutation analyses. Correlated mutations are visualized using heatmaps, or directly in protein structures using YASARA. Analyses of correlated mutations in various superfamilies showed that positions that correlate are often found in networks and that the positions in these networks often share a common function. Using these networks, mutants were predicted to increase the specificity or activity of proteins. Mutational studies confirmed that correlated mutation analyses are a valuable tool for rational design of proteins.

Mutator, the text mining tool used to incorporate mutations into 3DM systems is described in chapter 6. Mutator was designed to automatically retrieve mutations from literature and store these mutations in a 3DM system. A PubMed search using keywords from the 3DM system is used to preselect articles of interest. These articles are retrieved from the internet, converted to text, and parsed for mutations. Mutations are then grounded to proteins and stored in a 3DM database. Mutation retrieval was tested on the alpha-amylase superfamily as this superfamily contains the enzyme involved in Fabry’s disease: an x linked lysosomal storage disease. Compared to existing mutant databases, such as the HGMD and SwissProt, Mutator retrieved 30% more mutations from literature. A major problem in DNA diagnostics is the differentiation between natural variants and pathogenic mutations. To distinguish between pathogenic mutations and natural variation in proteins the Validator modules was added to 3DM. Validator uses the data available in a 3DM system to predict the pathogenicity of a mutant using, for example, the residue conservation of the mutants alignment position, side-chain accessibility of the mutant in the structure, and the number of mutations found in literature for the alignment position. Mutator and Validator can be used to study mutants found in disorder related genes. Although these tools are not the definitive solution for DNA diagnostics they can hopefully be used to increase our understanding of the molecular basis of disorders.

Chapter 7 and 8 describe applied research projects using 3DM systems containg proteins of potential commercial interest. A 3DM system for the a/b-beta hydrolases superfamily is described in chapter 7. This superfamily consists of almost 20,000 proteins with a diverse range of functions. Superfamily alignments were generated for the common beta-barrel fold shared by all superfamily members, and for five distinct subtypes within the superfamily. Due to the size and functional diversity of the superfamily, there is a lot of potential for industrial application of superfamily members. Chapter 8 describes a study focusing on a sucrose phosphorylase enzyme from the a-amylase superfamily. This enzyme can be potentially used in an industrial setting for the transfer of glucose to a wide variety of molecules. The aim of the study was to increase the stability of the protein at higher temperatures. A combination of rational design using a 3DM system, and in-depth study of the protein structure, led to a series of mutations that resulted in more than doubling the half-life of the protein at 60°C.

3DM systems have been successfully applied in a wide range of protein engineering and DNA diagnostics studies. Currently, 3DM systems are applied most successfully in project studying a single protein family or monogenetic disorder. In the future, we hope to be able to apply 3DM to more complex scenarios such as enzyme factories and polygenetic disorders by combining multiple 3DM systems for interacting proteins.

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