easyDAS: automatic creation of DAS servers.

BACKGROUND: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. RESULTS: Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. CONCLUSIONS: easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.

Two Doses of oxaliplatin with capecitabine (XELOX) in metastatic colorectal cancer.

PURPOSE: Phase II/III studies have shown XELOX to be as effective as FOLFOX in patients with advanced colorectal cancer (CRC). The study was designed to evaluate the activity and tolerability of XELOX in CRC. In August 2002, we began a prospective study of XELOX as first-line therapy for patients with metastatic CRC. Twenty-two patients were enrolled between November 2002 and August 2003 (series I). An interim analysis performed in August 2003 revealed that 32% of patients required a dose reduction of oxaliplatin because of toxicity. From August 2003 to April 2005, an additional 20 patients were included (series II). This second group of patients received oxaliplatin at a lower dose. PATIENTS AND METHODS: The first 22 patients (series I) included received oxaliplatin 130 mg/m(2) on day 1 plus capecitabine 2000 mg/m(2) daily on days 1-15 (3-week cycle). The second set of 20 patients (series II) received oxaliplatin 85 mg/m(2) on day 1; the dose of capecitabine and the frequency of administration were not modified. RESULTS: Patient characteristics were well balanced in the 2 series. Overall response (series I vs. II): 41% vs. 65%; median time to progression was similar: 10.51 vs. 10.92 (log-rank test, P = .79). Median survival was similar in the 2 series: 19.55 vs. 21.18 months (log-rank test, P = .61). Grade 3/4 toxicity (series I vs. II): peripheral neuropathy, 14% vs. 0 (P = .23). CONCLUSION: In patients with advanced CRC, in combination with capecitabine, oxaliplatin 85 mg/m(2) is as effective with lower toxicity when compared with oxaliplatin 130 mg/m(2).

GenExp: an interactive web-based genomic DAS client with client-side data rendering.

BACKGROUND: The Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse. RESULTS: Here we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on. CONCLUSIONS: GenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existing clients. It uses client-side data rendering techniques resulting in easier genome browsing and exploration. GenExp is open source under the GPL license and it is freely available at http://gralggen.lsi.upc.edu/recerca/genexp.