Stephan Symons

Mayday - integrative analytics for expression data

BackgroundDNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmers access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Maydays functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.ResultsWe have rewritten large parts of Maydays core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved.ConclusionsWe present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org.

Wound fluid lactate concentration: a helpful marker for diagnosing soft‐tissue infection in diabetic foot ulcers? Preliminary findings

Diabet. Med. 28, 175–178 (2011)

Do patient- and tumor-related factors predict the peritoneal spread of pancreatic adenocarcinoma?

PurposeIn pancreatic cancer, the presence of peritoneal carcinomatosis (PC) precludes the possibility of a surgical cure, irrespective of the resectability of the primary tumor. However, peritoneal spread cannot be reliably detected radiographically during preoperative tumor staging.MethodsThe pancreatic adenocarcinoma database of the Tübingen Comprehensive Cancer Center included 29 patients in whom PC was incidentally detected during the surgery. These patients were retrospectively compared for patient- and tumor-related factors with 29 randomly selected patients without PC who underwent curative resection.ResultsClinical jaundice and diarrhea were more frequently present in patients without PC. The CA 19-9 levels were significantly higher in patients with PC compared to those in patients without PC. No other differences were observed in the patient- or tumor-related factors between the two groups.ConclusionIn pancreatic cancer patients, markedly elevated CA 19-9 levels may serve as surrogate marker for peritoneal dissemination, irrespective of the local resectability of the tumor. In such patients, laparoscopy should be considered as an additional staging tool to rule out peritoneal carcinomatosis.

Experience after 100 patients treated with cytoreductive surgery and hyperthermic intraperitoneal chemotherapy

AIM To investigate perioperative patient morbidity/mortality and outcome after cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). METHODS Of 150 patients 100 were treated with cytoreductive surgery and HIPEC and retrospectively analyzed. Clinical and postoperative follow-up data were evaluated. Body mass index (BMI), age and peritoneal carcinomatosis index (PCI) were chosen as selection criteria with regard to tumor-free survival and perioperative morbidity for this multimodal therapy. RESULTS CRS with HIPEC was successfully performed in 100 out of 150 patients. Fifty patients were excluded because of intraoperative contraindication. Median PCI was 17 (1-39). In 89% a radical resection (CC0/CC1) was achieved. One patient died postoperatively due to multiorgan failure. Neither PCI, age nor BMI was a risk factor for postoperative complications/outcome according to the DINDO classification. In 9% Re-CRS with HIPEC was performed during the follow-up period. CONCLUSION Patient selection remains the most important issue. Neither PCI, age nor BMI alone should be an exclusion criterion for this multimodal therapy.

MGV: a generic graph viewer for comparative omics data

MOTIVATION High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones. RESULTS We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Maydays visual analytics capabilities by integrating a wide range of biological models, high-throughput data and meta information to display enriched graphs that combine data and models. A wide range of tools is available for visualization of nodes, data-aware graph layout as well as automatic and manual aggregation and refinement of the data. We show the usefulness of MGV applied to several problems, including differential expression of alternative transcripts, transcription factor interaction, cross-study clustering comparison and integration of transcriptomics and metabolomics data for pathway analysis. AVAILABILITY MGV is a open-source software implemented in Java and freely available as a part of Mayday at www.microarray-analysis.org/mayday. CONTACT symons@informatik.uni-tuebingen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

GaggleBridge: collaborative data analysis

MOTIVATION Tools aiding in collaborative data analysis are becoming ever more important as researchers work together over long distances. We present an extension to the Gaggle framework, which has been widely adopted as a tool to enable data exchange between different analysis programs on one computer. RESULTS Our program, GaggleBridge, transparently extends this functionality to allow data exchange between Gaggle users at different geographic locations using network communication. GaggleBridge can automatically set up SSH tunnels to traverse firewalls while adding some security features to the Gaggle communication. AVAILABILITY GaggleBridge is available as open-source software implemented in the Java language at http://it.inf.uni-tuebingen.de/gb. CONTACT florian.battke@uni-tuebingen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.