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Mark D Wilkinson

Publications and source records attributed to Mark D Wilkinson.

13 recordsLinked to original sources
PubMed2006

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

BACKGROUND: User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website. RESULTS: The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context. CONCLUSION: This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information.

Computational Biology↗
PubMed2006

BioMoby extensions to the Taverna workflow management and enactment software.

BACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. RESULTS: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. CONCLUSION: With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.

Biology↗
PubMed2006

The Life Sciences Semantic Web is full of creeps!

The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as 'semantic creep'-timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.

Computational Biology↗
PubMed2006

Fast, cheap and out of control: a zero curation model for ontology development.

During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose. The protocol used to create and evaluate this ontology involved a targeted, web-based interface. The design and implementation of this protocol is discussed along with quantitative and qualitative assessments of the constructed ontology.

Artificial Intelligence↗
PubMed2004

Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum.

BACKGROUND: Acetabularia acetabulum is a giant unicellular green alga whose size and complex life cycle make it an attractive model for understanding morphogenesis and subcellular compartmentalization. The life cycle of this marine unicell is composed of several developmental phases. Juvenile and adult phases are temporally sequential but physiologically and morphologically distinct. To identify genes specific to juvenile and adult phases, we created two subtracted cDNA libraries, one adult-specific and one juvenile-specific, and analyzed 941 randomly chosen ESTs from them. RESULTS: Clustering analysis suggests virtually no overlap between the two libraries. Preliminary expression data also suggests that we were successful at isolating transcripts differentially expressed between the two developmental phases and that many transcripts are specific to one phase or the other. Comparison of our EST sequences against publicly available sequence databases indicates that ESTs from the adult and the juvenile libraries partition into different functional classes. Three conserved sequence elements were common to several of the ESTs and were also found within the genomic sequence of the carbonic anhydrase1 gene from A. acetabulum. To date, these conserved elements are specific to A. acetabulum. CONCLUSIONS: Our data provide strong evidence that adult and juvenile phases in A. acetabulum vary significantly in gene expression. We discuss their possible roles in cell growth and morphogenesis as well as in phase change. We also discuss the potential role of the conserved elements found within the EST sequences in post-transcriptional regulation, particularly mRNA localization and/or stability.

Acetabularia↗
PubMed2003

FDG PET imaging of metastatic gastrointestinal stromal tumor.

A 75-year-old woman presented with an 8-month history of progressive abdominal distension and associated weight loss. Computed tomography (CT) showed a very large, partially enhancing, cystic/solid mass within the abdomen that extended from below the left diaphragm to the pelvis. A large (10 cm), partially enhancing lesion was also seen in segments 6 and 7 of the right lobe of the liver, consistent with metastatic disease. The patient underwent laparotomy and resection of a 5.7-kg abdominal tumor measuring 30 x 27 x 20 cm. Histology confirmed a gastrointestinal stromal tumor (GIST) of stomach origin. A whole-body F-18 fluorodeoxyglucose (FDG) positron emission tomography (PET) scan performed 2 months postoperatively demonstrated multiple glucose-avid lesions in the liver as well as residual disease within the abdomen and pelvis. The patient was referred to medical oncology. The authors give a brief overview of this rare mesenchymal tumor of the gastrointestinal tract and the potential role of PET.

Abdominal Neoplasms↗
PubMed2002

Transcripts of Vp-1 homeologues are misspliced in modern wheat and ancestral species.

The maize (Zea mays) Viviparous 1 (Vp1) transcription factor has been shown previously to be a major regulator of seed development, simultaneously activating embryo maturation and repressing germination. Hexaploid bread wheat (Triticum aestivum) caryopses are characterized by relatively weak embryo dormancy and are susceptible to preharvest sprouting (PHS), a phenomenon that is phenotypically similar to the maize vp1 mutation. Analysis of Vp-1 transcript structure in wheat embryos during grain development showed that each homeologue produces cytoplasmic mRNAs of different sizes. The majority of transcripts are spliced incorrectly, contain insertions of intron sequences or deletions of coding region, and do not have the capacity to encode full-length proteins. Several VP-1-related lower molecular weight protein species were present in wheat embryo nuclei. Embryos of a closely related tetraploid species (Triticum turgidum) and ancestral diploids also contained misspliced Vp-1 transcripts that were structurally similar or identical to those found in modern hexaploid wheat, which suggests that compromised structure and expression of Vp-1 transcripts in modern wheat are inherited from ancestral species. Developing embryos from transgenic wheat grains expressing the Avena fatua Vp1 gene showed enhanced responsiveness to applied abscisic acid compared with the control. In addition, ripening ears of transgenic plants were less susceptible to PHS. Our results suggest that missplicing of wheat Vp-1 genes contributes to susceptibility to PHS in modern hexaploid wheat varieties and identifies a possible route to increase resistance to this environmentally triggered disorder.

Alternative Splicing↗
PubMed2002

BioMOBY: an open source biological web services proposal.

BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services; data and services are decentralised, but the availability of these resources, and the instructions for interacting with them, are registered in a central location called MOBY Central. BioMOBY adds to the web services paradigm, as exemplified by Universal Data Discovery and Integration (UDDI), by having an object-driven registry query system with object and service ontologies. This allows users to traverse expansive and disparate data sets where each possible next step is presented based on the data object currently in-hand. Moreover, a path from the current data object to a desired final data object could be automatically discovered using the registry. Native BioMOBY objects are lightweight XML, and make up both the query and the response of a simple object access protocol (SOAP) transaction.

Computer Communication Networks↗
PubMed2002

The Bioperl toolkit: Perl modules for the life sciences.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

Algorithms↗
PubMedDate not supplied

Neuroimaging findings in a suprasellar granular cell tumor.

A 27-year-old woman presented with a history of amenorrhea, visual disturbance, and diabetes insipidus. Magnetic resonance imaging showed a large enhancing suprasellar mass with associated edema involving the left striatum. The lesion was hypometabolic on fluorodeoxyglucose-positron emission tomography. At surgery, a subtotal resection of a vascular tumor that appeared to arise from the posterior pituitary and hypothalamus was carried out. Pathologic examination revealed a granular cell tumor. We report the preoperative neuroimaging findings in this rare posterior pituitary stalk tumor.

Adult↗