A web services choreography scenario for interoperating bioinformatics applications

BACKGROUND: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. RESULTS: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). CONCLUSION: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow

MOWServ: a web client for integration of bioinformatic resources

The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/

Eccentric overload training in patients with chronic Achilles tendinopathy: a systematic review

Background: Eccentric overload training seems to be a promising conservative intervention in patients with chronic Achilles tendinopathy. The efficacy of eccentric overload training on the outcome measures of pain and physical functioning are not exactly clear. Study design: Systematic review of the literature. Methods: Electronic databases were searched for randomised clinical trials concerning eccentric overload training in patients with chronic Achilles tendinopathy. The Delphi list was used to assess the methodological quality of the studies. Results: Nine clinical trials were included. Only one study had sufficient methodological quality. The included trials showed an improvement in pain after eccentric overload training. Because of the methodological shortcomings of the trials, no definite conclusion can be drawn concerning the effects of eccentric overload training in patients with chronic Achilles tendinopathy. Conclusion: The effects of eccentric exercise training in patients with chronic Achilles tendinopathy on pain are promising; however, the magnitude of the effects cannot be determined. Large, methodologically sound studies from multiple sites in which functional outcome measures are included are warranted

Eccentric overload training in patients with a chronic Achilles tendinopathy: a systematic review.

Background: Eccentric overload training seems to be a promising conservative intervention in patients with chronic Achilles tendinopathy. The efficacy of eccentric overload training on the outcome measures of pain and physical functioning are not exactly clear. Study design: Systematic review of the literature. Methods: Electronic databases were searched for randomised clinical trials concerning eccentric overload training in patients with chronic Achilles tendinopathy. The Delphi list was used to assess the methodological quality of the studies. Results: Nine clinical trials were included. Only one study had sufficient methodological quality. The included trials showed an improvement in pain after eccentric overload training. Because of the methodological shortcomings of the trials, no definite conclusion can be drawn concerning the effects of eccentric overload training in patients with chronic Achilles tendinopathy. Conclusion: The effects of eccentric exercise training in patients with chronic Achilles tendinopathy on pain are promising; however, the magnitude of the effects cannot be determined. Large, methodologically sound studies from multiple sites in which functional outcome measures are included are warranted

Preoperatief fysiotherapeutisch trainingsprogramma voor oncologiepatiënten in Utrecht een MUST

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De Nederlandstalige Victorian Institute of Sports Assessment - Achilles (VISA-A) questionnaire: crossculturele adaptatie en validering bij Nederlandse patiënten met achilles tendinopathie

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Cross-culturele adaptatie van de Victorian Institute of Sports Assessment-Achilles tendon (VISA-A) vragenlijst en validering bij Nederlandse patiënten met een Achilles tendinopathie

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Feasibility and preliminary effectiveness of preoperative therapeutic exercise in patients with cancer: a pragmatic study.

The aim of this pilot study is to determine the feasibility and preliminary effectiveness of an individually designed preoperative therapeutic exercise program (PreTEP), in patients recently diagnosed with cancer and awaiting elective surgery. The purpose is to improve their physical fitness levels during this waiting period with the intention of decreasing postoperative morbidity. A preexperimental pilot study was performed at the University Medical Center Utrecht, The Netherlands. Thirty-nine patients diagnosed with cancer, scheduled for elective abdominal/thoracic surgery, were referred to a multidisciplinary preoperative screening. Fifteen patients (38%) participated in PreTEP. Participants were satisfied and motivated during the period of training (on average 5 weeks) in which they attended 84% of the sessions. Cardiorespiratory fitness (A strand-test) and muscle strength (Handheld Dynamometry) increased significantly, from 25 to 33 mL/kg/min, respectively (p<0.01; 95% confidence interval [CI]=-0.011 to -0.004) and from 894 Newton (N) to 961N (p<0.01; 95% CI=-94.53 to -39.0). No adverse events occurred during the training period. PreTEP was shown to be feasible, safe, and well-tolerated and appreciated by participants. Despite the relatively short period of training, physical fitness improved in all participants

Feasibility and preliminary effectiveness of preoperative therapeutic exercise in patients with cancer: a pragmatic study.

Item does not contain fulltextThe aim of this pilot study is to determine the feasibility and preliminary effectiveness of an individually designed preoperative therapeutic exercise program (PreTEP), in patients recently diagnosed with cancer and awaiting elective surgery. The purpose is to improve their physical fitness levels during this waiting period with the intention of decreasing postoperative morbidity. A preexperimental pilot study was performed at the University Medical Center Utrecht, The Netherlands. Thirty-nine patients diagnosed with cancer, scheduled for elective abdominal/thoracic surgery, were referred to a multidisciplinary preoperative screening. Fifteen patients (38%) participated in PreTEP. Participants were satisfied and motivated during the period of training (on average 5 weeks) in which they attended 84% of the sessions. Cardiorespiratory fitness (A strand-test) and muscle strength (Handheld Dynamometry) increased significantly, from 25 to 33 mL/kg/min, respectively (p<0.01; 95% confidence interval [CI]=-0.011 to -0.004) and from 894 Newton (N) to 961N (p<0.01; 95% CI=-94.53 to -39.0). No adverse events occurred during the training period. PreTEP was shown to be feasible, safe, and well-tolerated and appreciated by participants. Despite the relatively short period of training, physical fitness improved in all participants.1 februari 201