PDF Report Research Articles

MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers.

MicroRNAs (miRNAs) are small RNAs that regulate the expression of target mRNAs by specific binding on the mRNA 3'UTR and promoting mRNA degradation in the majority of cases. It is often of interest to know the specific targets of a miRNA in order to study them in a particular disease context. In that sense, some databases have been designed to predict potential miRNA-mRNA interactions based on hybridization sequences. However, one of the main limitations is that these databases have too many false positives and do not take into account disease-specific interactions. We have developed an R package (miRComb) able to combine miRNA and mRNA expression data with hybridization information, in order to find potential miRNA-mRNA targets that are more reliable to occur in a specific physiological or disease context. This article summarizes the pipeline and the main outputs of this package by using as example TCGA data from five gastrointestinal cancers (colon cancer, rectal cancer, liver cancer, stomach cancer and esophageal cancer). The obtained results can be used to develop a huge number of testable hypotheses by other authors. Globally, we show that the miRComb package is a useful tool to deal with miRNA and mRNA expression data, that helps to filter the high amount of miRNA-mRNA interactions obtained from the pre-existing miRNA target prediction databases and it presents the results in a standardised way (pdf report). Moreover, an integrative analysis of the miRComb miRNA-mRNA interactions from the five digestive cancers is presented. Therefore, miRComb is a very useful tool to start understanding miRNA gene regulation in a specific context. The package can be downloaded in http://mircomb.sourceforge.net.

NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.

Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving.Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK.Contact: richard.leggett@tgac.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

Advances in camera trap data management tools: Towards collaborative development and integration with GIS

Camera traps have become a widely used technique for conducting biological inventories, generating a large number of database records of great interest. The main aim of this paper is to describe a new free and open source software (FOSS), developed to facilitate the management of camera-trapped data which originated from a protected Mediterranean area (SE Spain). In the last decade, some other useful alternatives have been proposed, but ours focuses especially on a collaborative undertaking and on the importance of spatial information underpinning common camera trap studies.This FOSS application, namely, “Camera Trap Manager” (CTM), has been designed to expedite the processing of pictures on the .NET platform. CTM has a very intuitive user interface, automatic extraction of some image metadata (date, time, moon phase, location, temperature, atmospheric pressure, among others), analytical (Geographical Information Systems, statistics, charts, among others), and reporting capabilities (ESRI Shapefiles, Microsoft Excel Spreadsheets, PDF reports, among others). Using this application, we have achieved a very simple management, fast analysis, and a significant reduction of costs. While we were able to classify an average of 55 pictures per hour manually, CTM has made it possible to process over 1000 photographs per hour, consequently retrieving a greater amount of data.

SU‐E‐T‐596: P3DVHStats ‐ a Novel, Automatic, Institution Customizable Program to Compute and Report DVH Quantities On Philips Pinnacle TPS

Purpose:To implement a novel, automatic, institutional customizable DVH quantities evaluation and PDF report tool on Philips Pinnacle treatment planning system (TPS)Methods:An add‐on program (P3DVHStats) is developed by us to enable automatic DVH quantities evaluation (including both volume and dose based quantities, such as V98, V100, D2), and automatic PDF format report generation, for EMR convenience. The implementation is based on a combination of Philips Pinnacle scripting tool and Java language pre‐installed on each Pinnacle Sun Solaris workstation. A single Pinnacle script provide user a convenient access to the program when needed. The activated script will first export DVH data for user selected ROIs from current Pinnacle plan trial; a Java program then provides a simple GUI interface, utilizes the data to compute any user requested DVH quantities, compare with preset institutional DVH planning goals; if accepted by users, the program will also generate a PDF report of the results and export it from Pinnacle to EMR import folder via FTP.Results:The program was tested thoroughly and has been released for clinical use at our institution (Pinnacle Enterprise server with both thin clients and P3PC access), for all dosimetry and physics staff, with excellent feedback. It used to take a few minutes to use MS‐Excel worksheet to calculate these DVH quantities for IMRT/VMAT plans, and manually save them as PDF report; with the new program, it literally takes a few mouse clicks in less than 30 seconds to complete the same tasks.Conclusion:A Pinnacle scripting and Java language based program is successfully implemented, customized to our institutional needs. It is shown to dramatically reduce time and effort needed for DVH quantities computing and EMR reporting.

SU-D-BRD-03: Improving Plan Quality with Automation of Treatment Plan Checks

Purpose: To evaluate the effectiveness of an automated plan check tool to improve first-time plan quality as well as standardize and document performance of physics plan checks. Methods: The Plan Checker Tool (PCT) uses the Eclipse Scripting API to check and compare data from the treatment planning system (TPS) and treatment management system (TMS). PCT was created to improve first-time plan quality, reduce patient delays, increase efficiency of our electronic workflow, and to standardize and partially automate plan checks in the TPS. A framework was developed which can be configured with different reference values and types of checks. One example is the prescribed dose check where PCT flags the user when the planned dose and the prescribed dose disagree. PCT includes a comprehensive checklist of automated and manual checks that are documented when performed by the user. A PDF report is created and automatically uploaded into the TMS. Prior to and during PCT development, errors caught during plan checks and also patient delays were tracked in order to prioritize which checks should be automated. The most common and significant errors were determined. Results: Nineteen of 33 checklist items were automated with data extracted with the PCT. These include checks formore » prescription, reference point and machine scheduling errors which are three of the top six causes of patient delays related to physics and dosimetry. Since the clinical roll-out, no delays have been due to errors that are automatically flagged by the PCT. Development continues to automate the remaining checks. Conclusion: With PCT, 57% of the physics plan checklist has been partially or fully automated. Treatment delays have declined since release of the PCT for clinical use. By tracking delays and errors, we have been able to measure the effectiveness of automating checks and are using this information to prioritize future development. This project was supported in part by P01CA059827.« less

TU-AB-201-02: An Automated Treatment Plan Quality Assurance Program for Tandem and Ovoid High Dose-Rate Brachytherapy

Purpose: For tandem and ovoid (T&O) HDR brachytherapy in our clinic, it is required that the planning physicist manually capture ∼10 images during planning, perform a secondary dose calculation and generate a report, combine them into a single PDF document, and upload it to a record- and-verify system to prove to an independent plan checker that the case was planned correctly. Not only does this slow down the already time-consuming clinical workflow, the PDF document also limits the number of parameters that can be checked. To solve these problems, we have developed a web-based automatic quality assurance (QA) program. Methods: We set up a QA server accessible through a web- interface. A T&O plan and CT images are exported as DICOMRT files and uploaded to the server. The software checks 13 geometric features, e.g. if the dwell positions are reasonable, and 10 dosimetric features, e.g. secondary dose calculations via TG43 formalism and D2cc to critical structures. A PDF report is automatically generated with errors and potential issues highlighted. It also contains images showing important geometric and dosimetric aspects to prove the plan was created following standard guidelines. Results: The program has been clinically implemented in our clinic. In each of the 58 T&O plans we tested, a 14- page QA report was automatically generated. It took ∼45 sec to export the plan and CT images and ∼30 sec to perform the QA tests and generate the report. In contrast, our manual QA document preparation tooks on average ∼7 minutes under optimal conditions and up to 20 minutes when mistakes were made during the document assembly. Conclusion: We have tested the efficiency and effectiveness of an automated process for treatment plan QA of HDR T&O cases. This software was shown to improve the workflow compared to our conventional manual approach.

WE-D-204-06: An Open Source ImageJ CatPhan Analysis Tool

Purpose: The CatPhan is a popular QA device for assessing CT image quality. There are a number of software options which perform analysis of the CatPhan. However, there is often little ability for the user to adjust the analysis if it isn't running properly, and these are all expensive options. An open source tool is an effective solution. Methods: To use the software, the user imports the CT as an image sequence in ImageJ. The user then scrolls to the slice with the lateral dots. The user then runs the plugin. If tolerance constraints are not already created, the user is prompted to enter them or to use generic tolerances. Upon completion of the analysis, the plugin calls pdfLaTex to compile the pdf report. There is a csv version of the report as well. A log of the results from all CatPhan scans is kept as a csv file. The user can use this to baseline the machine. Results: The tool is capable of detecting the orientation of the phantom. If the CatPhan was scanned backwards, one can simply flip the stack of images horizontally and proceed with the analysis. The analysis includes Sensitometry (estimating the effective beam energy), HU values and linearity, Low Contrast Visibility (using LDPE & Polystyrene), Contrast Scale, Geometric Accuracy, Slice Thickness Accuracy, Spatial resolution (giving the MTF using the line pairs as well as the point spread function), CNR, Low Contrast Detectability (including the raw data), Uniformity (including the Cupping Effect). Conclusion: This is a robust tool that analyzes more components of the CatPhan than other software options (with the exception of ImageOwl). It produces an elegant pdf and keeps a log of analyses for long-term tracking of the system. Because it is open source, users are able to customize any component of it.

NI-79 * RAPID ASSESSMENT OF LESION VOLUMES FOR PATIENTS WITH GLIOMA USING THE SMARTBRUSH SOFTWARE PACKAGE

The increasing interest in enhancing the RANO criteria by using quantitative assessments of changes in lesion size and image intensities has highlighted the need for rapid, easy-to-use tools that provide DICOM compatible outputs for evaluation of patients with glioma. To evaluate the performance of the SmartBrush software (Brainlab AG), which provides computer-assisted definitions of regions of interest (ROIs), a cohort of 20 patients with glioma (equal number having high and low grade and treated and un-treated) were scanned using a 3T whole-body MR system prior to surgical resection. The T2-weighted FLAIR, pre- and post-contrast T1-weighted gradient echo DICOM images were pushed from the scanner to an offline workstation where analysis of lesion volumes was performed using SmartBrush. Volumes of the T2Ls ranged from 7.9 to 110.2cm3 and the volumes of the CELs was 0.1 to 28.5 cm3 with 19/20 of the subjects having CELs and all 20 having T2Ls. the computer-assisted analysis was performed rapidly and efficiently, with the mean time for defining both lesions per subject was 5.77 (range 3.5 to 7.5) minutes. Prior analysis of ROIS with the SLICER package (www.slicer.org) took approximately 30 minutes/subject. SmartBrush provides lesion volumes and cross-sectional diameter as a PDF report, which can be stored in DICOM. The ROIs were also saved as DICOM objects and transferred to other packages for performing histogram analysis from ADC or other functional parameter maps. Ongoing studies that will be reported in this presentation are performing a similar analysis with multiple users in order to compare the relative intra- and inter-operator variations in terms of both the speed of analysis and the ROIs that are identified. Acknowledgements: The authors would like to acknowledge Rowena Thomson and Natalie Wright from Brainlab for helping to set up this study.

Incorporation of externally generated next-generation tumor genotyping into clinical and research workflows: Successes and lessons learned.

156 Background: The future of oncology will increasingly utilize information about tumor genomics. A growing number of tumor subtypes require genomic information as standard of care to inform treatment decisions. Clinical decision support (CDS) systems are able to improve healthcare and ensure best practices, but rely on machine-readable data. Typically, 3rd party genotyping results are returned in PDF reports that are not computable for standard presentation, CDS, or research purposes. Proposed oncology CDS platforms (such as CancerLinQ) will require computable tumor genomic information. Methods: A 3rd party CLIA-certified laboratory performed targeted exome tumor sequencing for a subset of cancer patients seen at Vanderbilt University (VUMC). The variants considered “actionable” were packaged into a standardized extensible markup language (XML) message and transmitted securely to a clinical server on a daily basis; the full PDF report was also transferred electronically. These messages were automatically received and parsed to match patients and display mutation data in their electronic medical record (EMR) for clinicians. This information was also placed into the VUMC Research Derivative (see Danciu et al. J Biomed Inform 2014 for more details). Results: The XML message, including specimen metadata, was successfully created by the 3rd party lab and received by VUMC after an iterative testing process was conducted. Clinicians were notified automatically when results were ready, within their EMR workflow. Because the primary purpose of the test is clinical, variants of unknown significance were not included in the XML transfer (these were however available in the PDF report). Conclusions: To our knowledge, this is the first demonstration of the automated incorporation of tumor genotype information from a 3rd party lab into a clinical EMR. Electronic transfer of genotype data enables rapid consumption of results by clinicians within their standard workflow, passive CDS (e.g. pointers to external knowledge bases), active CDS (e.g. standard and clinical trial treatment recommendations), and secondary use: all activities that improve the quality of cancer care.

New wwPDB validation pipelines for X-ray, NMR and 3DEM structures

The Protein Data Bank (PDB) is the single global archive of 3D biomacromolecular structure data. The archive is managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org) organisation through its partners, the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank Japan (PDBj), the Protein Data Bank in Europe and the Biological Magnetic Resonance Bank (BMRB). Analogously, the Electron Microscopy Data Bank (EMDB) is managed by the EMDataBank (emdatabank.org) organisation. A few years ago, realising the needs and opportunities to assess the quality of biomacromolecular structures deposited in the PDB, the wwPDB and EMDataBank partners established Validation Task Forces (VTFs) to advice them on up-to-date and community-agreed methods and standards to validate X-ray, NMR and 3DEM structures and data. All three VTFs have now published their recommendations (1, 2, 3) and these are getting implemented as validation-software pipelines . The pipelines are integrated in the new joint wwPDB deposition and annotation system (http://deposit.wwpdb.org/deposition/). In addition, stand-alone servers are provided to allow practising structural biologists to validate models prior to publication and deposition (http://wwpdb.org/validation-servers.html). The validation pipelines and the output they produce (human-readable PDF reports and machine-readable XML files) will be described.

Issues with the communication and integrity of audit reports when financial reporting shifts to an information-centric paradigm

A core application of XBRL is to facilitate the flow of tagged financial statements and annual reports, from companies and other entities directly to the databases, web sites, and computers of regulators, stakeholders and other information consumers. Increasingly, XBRL provides the technological foundation for the communication of financial information where there is independent assurance. This XBRL-based assurance may be on the financial statements (i.e., an electronically consumable form of today's standard PDF or HTML audit report) or focus on the quality of the XBRL exhibit (i.e., the instance document). Regardless of the type of XBRL assurance report, maintenance of the security and integrity of the instance document is paramount. This conceptual paper identifies and discusses the communication, security challenges and relevant research issues when there is independent assurance on financial statements formatted in XBRL. Successful electronic communication of assurance to information consumers should clearly distinguish the responsibilities of management (i.e., the financial statements) and the auditor (i.e., the audit report). It is important to have an integrated approach where the assurance report, financial statements and other reports in which facts in the financial statements are incorporated are inextricably tied at the level of automated data consumption. Further, as much as possible, human interaction should be accommodated. The paper sets out a range of alternatives for maintenance of security on the assurance report.

SU‐E‐T‐503: Development of a Software Tool for Verification of Delivered Tomotherapy Plans Using the Tomo Log File

Purpose:The data receive server (DRS) in the Tomotherapy Unit records planned and actually delivered plan parameters for each treatment into a log file. The purpose of this study was to develop a software tool using the log file for verification of the patient plan delivered during treatment.Methods:A software tool, TomoPQA, was developed using the Python programming language. The software was implemented using object‐oriented methodology and modular design. The program has three built‐in modules: Read‐in module for loading the log file, analysis module for analyzing the log file and reporting module for producing a PDF report.Results:The developed software tool can be used to monitor and check the following plan parameters during patient treatment: (1) planned and actual field width; (2) planned and actual treatment time; (3) planned and actual couch speed; (4) planned and actual gantry speed; (4) planned and actual setup position. The software shows the difference between these parameters as a graphic plot against each treatment fraction in a PDF report for easy review or these values can be exported to an excel file. The program can process a 100M byte log file and produce a report in the order of one minute and can run on Windows, Linux or Mac platforms as a standalone program. A server version of this program can also be implemented for full automation of the log file processing, generation of the PDF report and also has the potential for an automated email if given values are out of tolerance.Conclusion:A QA software tool has been developed for in‐vivo quality assurance of treatment delivered on a Tomotherapy Unit. This tool provides an independent verification of the difference between actual delivered and planned parameters during treatment.

PopGenReport: simplifying basic population genetic analyses in R

Summary Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve. PopGenReport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating function. The function popgenreport allows users to perform up to 13 pre‐defined and 1 user‐defined analyses through the use of a single command line. Each analysis generates figures and tables that are incorporated into a pdf report and are also made available as individual files (figures are provided in multiple formats, table contents are provided as csv files). The package includes new R functions that simplify the importation of data from a spreadsheet file, examine allele distributions across populations and loci and identify private alleles, determine pairwise individual genetic distances using the methods of Smouse and Peakall () and Kosman and Leonard (), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (). The package has a modular structure that makes the process of adding new functionality straightforward. To facilitate the addition of user‐designed functions, the package includes a fully customizable module that can be automatically included in the pdf report. To support users not experienced in R, the website (www.popgenreport.org) has a tutorial for the package and a downloadable, portable version of the package with LaTeX pre‐configured for the Windows operating system.

Novel NMR-Technology to Assess Food Quality and Safety

High Resolution NMR Spectroscopy offers unique screening capabilities for food quality and safety by combining untargeted and targeted screening in one analysis. The objective of this contribution is to demonstrate, that due to its extreme reproducibility NMR can detect smallest changes in concentrations of many components in a mixture, which is best monitored by statistical evaluation however also delivers reliable quantification results. The methodology typically uses a 400 MHz high resolution instrument under full automation after minimized sample preparation, which in the case of aqueous solution just needs buffering to adjust pH and in case of cloudy samples centrifugation. For example one fruit juice analysis in a push button operation takes at maximum 15 minutes and delivers a multitude of results, which are automatically summarized in a PDF report. The method has been proven on fruit juices, where so far unknown frauds could be detected. In addition conventional targeted parameters are obtained in the same analysis. This technology has the advantage, that NMR is completely quantitative and concentration calibration only has to be done once for all compounds. Since NMR is so reproducible, it is also transferable between different instruments of the same field strength and different laboratories. Based on strict SOP`s, statistical models developed once can be used on multiple instruments and strategies for compound identification and quantification are applicable as well across labs. This technology is currently extended to other food materials as well, like for example wine, edible oils, honey and milk powder and examples for all food materials mentioned are given. On fruit juices and baby milk powder it could be proven, that food quality and safety can be brought to a new comprehensive level , that allows to answer many more questions than conventional analysis so far could deliver.

Critical components testing using hybrid genetic algorithm

As quality of software plays a vital role in real time systems, it is essential to identify the crucial parts in the system and to test them effectively. In the proposed approach, the critical components are identified by means of mutation based impact analysis. The next task is to test the critical components using the Hybrid Genetic Algorithm (HGA) based test case generation and optimization approach. The mutants are automatically generated by seeding faults into each method of all the components in the Software Under Test (SUT). The initial set of test cases is generated using randomized test data. The generated test cases are executed over the original and the mutant to identify whether the test case detects the error or not. Based on the results, the Mutation Score (MS) is calculated, which always lies between 0 and 1. The best test cases are chosen based on having higher mutation scores and are executed on mutants to analyze how each component affects the other components in the SUT. Based on the analysis, the critical components are identified and they need rigorous testing using the test cases generated by the HGA. The algorithm uses the RemoveTop and LocalBest improvement heuristics to achieve near optimal solutions. In unit testing, the test cases are executed against the original and the mutant. The test case optimization is done by evaluating the effectiveness of test suites using the Mutation Score and the Branch Coverage Value (BCV). In pair-wise testing, the effective test cases are selected based on the higher mutation scores and branch coverage values. The components are executed against these test cases and the execution traces are recorded. The traced results are compared against the expected outputs which were previously stored in the repository and the statuses are updated. Based on the statuses, the faulty methods are revealed. The efficiency of the proposed approach is compared with Genetic Algorithm (GA) and we concluded that the final test suite size and the total execution time are reduced in the proposed approach. Finally various graphs and PDF reports are generated for visualization purposes.

Kubios HRV – Heart rate variability analysis software

Kubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data. It includes an adaptive QRS detection algorithm and tools for artifact correction, trend removal and analysis sample selection. The software computes all the commonly used time-domain and frequency-domain HRV parameters and several nonlinear parameters. There are several adjustable analysis settings through which the analysis methods can be optimized for different data. The ECG derived respiratory frequency is also computed, which is important for reliable interpretation of the analysis results. The analysis results can be saved as an ASCII text file (easy to import into MS Excel or SPSS), Matlab MAT-file, or as a PDF report. The software is easy to use through its compact graphical user interface. The software is available free of charge for Windows and Linux operating systems at http://kubios.uef.fi.

AN EXPLANATION FACILITY FRAMEWORK FOR RULE-BASED SYSTEMS

Rule engines, business rule management systems and other rule-based systems used today widely utilize methods, techniques and technologies from the era of expert systems. Unfortunately, this doesn't seem to be the case when it comes to explanation facilities. Nowadays, the use of explanation facilities seems more important than ever. Business rule management systems control or constrain the behavior of business processes through business rules and an explanation of the inference process intended for the end user would be more than welcome. An explanation facility framework which was created in order to remedy this situation is presented in this paper. It is written in Java and is supposed to be a generic solution for modern rule-based systems. Besides being free and open-source, it is simple to use and can generate explanations in the form of natural language like sentences. Internationalization is also supported and explanations can be saved as textual, XML or PDF reports.

SU‐E‐T‐176: A Web Based Tool for the Implementation of Routine Linac QA Following TG1 42

Purpose: To develop a web environment where the TG142 proposed test actions and results can be entered and retrieved for review and electronic approval. Methods and Materials: AAPM Task Group 142 published recently a report with recommendations and tests for a comprehensive quality assurance program for external beam radiation therapy for linear accelerators. The recommendations address frequency and tolerances for the proposed tests. In addition, there are qualifiers for tests that are specific to linacs that are used for IMRT and stereotactic procedures. We have developed a web based environment using the asp.net tools where the TG142 tests have been implemented for the recommended frequencies for seven different linear accelerators in our institution. The end user (therapist or medical physicist) has a unique login and password and follows the prompts of the web page to complete each test. Baselines and tolerances are built into the program and data analysis is performed automatically, reporting a pass or fail result. Data trend analysis can be plotted and the medical physicist can review and approve the qa results electronically. The pdf report of the qa analysis can be printed or uploaded to the RV system as part of an EMR QA environment. Results: We have implemented this web based QA tool in our department with great success. The sequence ofmorning qa tasks has also been optimized so that the entire suite of tests per TG142 takes no more than 20min to perform. Electronic approval of the QA is available only to the faculty physicist. Once the document is approved, it is automatically uploaded to Mosaiq under the patient name corresponding to the machine name. Conclusion: A web based TG142 qa tool was developed and implemented in our clinic, allowing for data entry, analysis, trend plotting and electronic approval.

Free-Wilson in the 21st Century – evolution of a versatile toolkit for SAR analysis

When drug discovery projects are transferred, then rapidly assessing the available SAR in both overview and in numerical detail is a prerequisite for effective computational chemistry input. Following multiple company acquisitions, regular requirements for the approach has led to an effective and fast platform for Free-Wilson [1] based SAR review: in fact the utility is sufficient that it can for a useful reporting or project browsing tool for the busy modeller. Figure ​Figure11 Figure 1 In this talk it is shown how a carefully crafted PDF report can be combined with “on the fly” Matched Molecular Pair [2] and other drill downs to provide a versatile platform for SAR exploration and presentation that is appealing and to medicinal chemists.

Harvesting maps on the web

Maps are one of the most valuable documents for gathering geospatial information about a region. Yet, finding a collection of diverse, high-quality maps is a significant challenge because there is a dearth of content-specific metadata available to identify them from among other images on the Web. For this reason, it is desirous to analyze the content of each image. The problem is further complicated by the variations between different types of maps, such as street maps and contour maps, and also by the fact that many high-quality maps are embedded within other documents such as PDF reports. In this paper, we present an automatic method to find high-quality maps for a given geographic region. Not only does our method find documents that are maps, but also those that are embedded within other documents. We have developed a Content-Based Image Retrieval (CBIR) approach that uses a new set of features for classification in order to capture the defining characteristics of a map. This approach is able to identify all types of maps irrespective of their subject, scale, and color in a highly scalable and accurate way. Our classifier achieves an F1-measure of 74%, which is an 18% improvement over the previous work in the area.