Biomedical subjects

Tim Carver

Publications and source records attributed to Tim Carver.

5 recordsLinked to original sources

PubMed2025

Psychological and emotional impacts of communicating breast cancer risk using multifactorial assessment with polygenic risk score: Findings from PERSPECTIVE I&I.

PURPOSE: To examine the psychological and emotional outcomes of personalized breast cancer risk communication up to 1 year after disclosure in a risk-stratified breast screening preimplementation study (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation). METHODS: Among 3753 females aged 40 to 69, unaffected by breast cancer, with a prior mammogram, and who underwent multifactorial risk assessment to estimate their 10-year breast cancer risk, 2734 completed follow-up questionnaires up to 1 year after risk communication: 78.5% were at average risk, 16.5% at higher than average risk, and 5.0% at high risk. The impact of risk communication on breast cancer worry and psychological distress and factors associated with decisional regret were examined. RESULTS: Breast cancer worry and psychological distress scores remained low after risk communication and at 1 year follow-up. Up to 1 year after disclosure, small significant differences in breast cancer worry were observed between risk levels. Decisional regret was very low 1 year after risk communication. Lower levels of decisional regret were significantly associated with some factors, including higher satisfaction with the information received. CONCLUSION: This study suggests that personalized breast cancer risk communication has low negative psychological and emotional effects and highlights the importance of the information received for implementing this approach at population level.

Humans↗

PubMed2004

Taverna: a tool for the composition and enactment of bioinformatics workflows.

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

Computational Biology↗

PubMed2004

Pelican: pedigree editor for linkage computer analysis.

SUMMARY: Linkage analysis software requires an input text file that describes the structure of the pedigrees to be analysed. Manual creation of these files is tedious and error-prone, and a graphical input tool is desirable. This is currently only available in commercial packages that include much greater functionality. We have therefore developed Pelican, a lightweight graphical pedigree editor for rapid construction of linkage pedigree files and diagrams. AVAILABILITY: The software runs on any Java-enabled machine (version 1.2 or higher). A Java Web Start launch, class files, a demonstration applet, source code and documentation are freely available at http://www.rfcgr.mrc.ac.uk/Software/PELICAN/

Chromosome Mapping↗

PubMed2004

Molecular characterisation of the SAND protein family: a study based on comparative genomics, structural bioinformatics and phylogeny.

The activities of vertebrate lysosomes are critical to many essential cellular processes. The yeast vacuole is analogous to the mammalian lysosome and is used as a tool to gain insights into vesicle mediated vacuolar/lysosome transport. The protein SAND, which does not contain a SAND domain (PFAM accession number PF01342), has recently been shown to function at the tethering/docking stage of vacuole fusion as a critical component of the vacuole SNARE complex. In this publication we have identified SAND in diverse eukaryotes, from single celled organisms such as the yeasts to complex multi-cellular chordates such as mammals. We have demonstrated subfamily divisions in the SAND proteins and show that in vertebrates, a duplication event gave rise to two SAND sequences. This duplication appears to have occurred during early vertebrate evolution and conceivably with the evolution of lysosomes. Using bioinformatics we predict a secondary structure, solvent accessibility profile and protein fold for the SAND proteins and determine conserved sequence motifs, present in all SAND proteins and those that are specific to subsets. A comprehensive evaluation of yeast and human functional studies in conjunction with our in silico analysis has identified potential roles for some of these motifs.

Amino Acid Sequence↗

PubMed2003

The design of Jemboss: a graphical user interface to EMBOSS.

DESIGN: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/

Computer Graphics↗