Standard File Format Research Articles

LibSBGN: Electronic Processing of SBGN maps

AbstractIntroduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations. Results To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.

MrBac: A web server for draft metabolic network reconstructions for bacteria

Genome-scale metabolic network reconstruction can be used for simulating cellular behaviors by simultaneously monitoring thousands of biochemical reactions, and is therefore important for systems biology studies in microbes. However, the labor-intensive and time-consuming reconstruction process has hindered the progress of this important field. Here we present a web server, MrBac (Metabolic network Reconstructions for Bacteria), to streamline the network reconstruction process for draft genome-scale metabolic networks and to provide annotation information from multiple databases for further curation of the draft reconstructions. MrBac integrates comparative genomics, retrieval of genome annotations, and generation of standard systems biology file format ready for network analyses. We also used MrBac to automatically generate a draft metabolic model of Salmonella enteric serovar Typhimurium LT2. The high similarity between this automatic model and the experimentally validated models further supports the usefulness and accuracy of MrBac. The high efficiency and accuracy of MrBac may accelerate the advances of systems biology studies on microbiology. MrBac is freely available at http://sb.nhri.org.tw/MrBac.

Visual data exploration for hydrological analysis

Hydrological research projects for integrated water resources management such as the IWAS initiative often accumulate large amounts of heterogeneous data from different sources. Given the number of partners taking part in such projects, surveying and accessing the available data sets, as well as searching for a defined subset, becomes increasingly difficult. We propose an integrated approach for a system combining visual data management and numerical simulation which allows to survey and select data sets based on keywords such as a region of interest or given indicators. An adequate 3D visualisation of such subsets helps to convey information and significantly supports the assessment of relations between different types of data. Furthermore, the interface between the visual data management system and finite element codes allows for the straightforward integration of information into the numerical simulation process and the subsequent visualisation of simulation results in a geographical context. We demonstrate typical workflows for integration and processing within the system based on data from the IWAS model region in Saudi Arabia and the TERENO Bode Observatory in the Harz Mountains in Germany. In addition, we present examples for data import and export based on established standard file formats.

TLM-Converter: Reorganization of Long Time-Lapse Microscopy Datasets for DownStream Image Analysis

Automated microscopy enables in vivo studies in developmental biology over long periods of time. Time-lapse recordings in three or more dimensions to study the dynamics of developmental processes can produce huge data sets that extend into the terabyte range. However, depending on the available computational resources and software design, downstream processing of very large image data sets can become highly inefficient, if not impossible. To address the lack of available open source and commercial software tools to efficiently reorganize time-lapse data on a desktop computer with limited system resources, we developed TLM-Converter. The software either fragments oversized files or concatenates multiple files representing single time frames and saves the output files in open standard formats. Our application is undemanding on system resources as it does not require the whole data set to be loaded into the system memory. We tested our tool on time-lapse data sets of live Drosophila specimens recorded by laser scanning confocal microscopy. Image data reorganization dramatically enhances the productivity of time-lapse data processing and allows the use of downstream image analysis software that is unable to handle large data sets of ≥2 GB. In addition, saving the outputs in open standard image file formats enables data sharing between independently developed software tools.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/.

Efficient application programming interface for multi-dimensional modeling data

This paper describes an Application Programming Interface (API) for managing multi-dimensional data produced for water resource computational modeling that is being developed by the US Army Engineer Research and Development Center (ERDC), in conjunction with Brigham Young University. This API, along with a corresponding data standard, is being implemented within ERDC computational models to facilitate rapid data access, enhanced data compression and data sharing, and cross-platform independence. The API and data standard are known as the eXtensible Model Data Format (XMDF), and version 1.3 is available for free download. This API is designed to manage geometric data associated with grids, meshes, riverine and coastal cross sections, and both static and transient array-based datasets. The inclusion of coordinate system data makes it possible to share data between models developed in different coordinate systems. XMDF is used to store the data-intensive components of a modeling study in a compressed binary format that is platform-independent. It also provides a standardized file format that enhances modeling linking and data sharing between models.

Focus on lasers and imaging

Focus on lasers and imaging

Overview of the CCP4 suite and current developments.

The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

BackgroundBioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts.ResultsTo enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats).ConclusionsPaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples.

EasyDAS: Automatic creation of DAS servers

BackgroundThe 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.ResultsHere 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.ConclusionseasyDAS 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.

The MPEG Interactive Music Application Format Standard [Standards in a Nutshell

The music industry is going through a transformation, and new interactive music services have emerged. It is envisaged that this new concept of digital music content will dominate the next generation of music services. A standardized file format is inevitably required to provide the interoperability between various interactive music players and interactive music albums. This issue is addressed in a new standard by the Moving Picture Experts Group (MPEG), known as the MPEG-A Interactive Music Application Format (IM AF). IM AF integrates multiple audio tracks with appropriate additional information, enabling users to experience various preset mixes and to make their own mixes complying with interactivity rules imposed by the music composers with the aim of fitting their artistic creation.

Comparison of Programmatic Approaches for Efficient Accessing to mzML Files

The Human Proteome Organization (HUPO) Proteomics Standard Initiative has been tasked with developing file formats for storing raw data (mzML) and the results of spectral processing (protein identification and quantification) from proteomics experiments (mzIndentML). In order to fully characterize complex experiments, special data types have been designed. Standardized file formats will promote visualization, validation and dissemination of data independent of the vendor-specific binary data storage files. Innovative programmatic solutions for robust and efficient data access to standardized file formats will contribute to more rapid wide-scale acceptance of these file formats by the proteomics community.In this work, we compare algorithms for accessing spectral data in the mzML file format. As an XML file, mzML files allow efficient parsing of data structures when using XML-specific class types. These classes provide only sequential access to files. However, random access to spectral data is needed in many algorithmic applications for processing proteomics datasets. Here, we demonstrate implementation of memory streams to convert a sequential access into random access. Our application preserves the elegant XML parsing capabilities. Benchmarking file access times in sequential and random access modes show that while for small number of spectra the random access is more time efficient, when retrieving large number of spectra sequential access becomes more efficient. We also provide comparisons to other file accessing methods from academia and industry.

Virtual bronchoscopy in the fetus

The term ‘virtual bronchoscopy’ describes the creation and evaluation of representations of the bronchial tree and surrounding structures using spatial information derived from imaging sources other than the bronchoscope itself. Initially, this referred to two-dimensional and later three-dimensional (3D) bronchial tree representations generated from computed tomography images. However, virtual bronchoscopy can now also be performed using data from magnetic resonance imaging (MRI). Several software options are available that can be used to generate accurate and realistic renderings of the bronchial tree 1–3 . Advances in imaging technology have led to vast improvements in fetal evaluation. Ultrasound examination is the primary method of fetal assessment because it is patient-friendly, effective, cost-efficient and considered to be safe 4 . MRI is generally used when ultrasound cannot provide sufficiently high-quality images. It offers high-resolution fetal imaging with excellent contrast that allows visualization of internal tissues 5 .I n this article we describe virtual bronchoscopy performed in a normal fetus that underwent MRI at 28 weeks’ gestation due to placenta previa with suspicion of placenta accreta. MRI examination was performed using a 1.5-T scanner (Siemens, Erlangen, Germany). The protocol involved a T2-weighted sequence in the three planes of the fetal body (HASTE; repetition time (TR), shortest; echo time (TE), 140 ms; field of view, 300–200 mm; matrix, 256 × 256; slice thickness, 4 mm; acquisition time, 17 s; 40 slices). In addition, we applied a 3D, T2-weighted TrueFISP sequence in the sagittal plane (TRUFI; TR/TE = 3.02/1.34; voxel size 1.6 × 1.6 × 1. 6m m 3 ; flip angle = 70 ◦ ; parallel acquisition techniques 2; acquisition time, 0.26 s) (Figure 1). The entire examination time did not exceed 20 min. The 3D MRI datasets were reconstructed to produce an interactive surface model of the fetal respiratory tract that could be viewed from any angle. Firstly, a 3D model of the fetal airway was created from the overlapping image layers generated by MRI using the software Mimics (Materialise, Leuven, Belgium), which allowed the surface of the airway to be delineated using contrast detection in the relevant areas of interest. The 3D model that was generated was exported using the standard triangular language file format and then converted into an OBJ file using the MAYA 3D modeling software (Autodesk, San Rafael, CA, USA) 6,7 . This program allows the virtual positioning of observation cameras while working with multiple on-screen windows. After the development of the 3D model, the software allows the user to determine the best positioned viewpoints for visualization of the 3D model (Figure 2) and also facilitates the adjustment of lighting parameters to improve contrast resolution. Using the navigation mode it is also possible to perform virtual bronchoscopy to visualize the upper respiratory tract from the pharynx downwards through the tracheobronchial tree (Videoclip S1) with a quality similar to that which could be obtained by videotaped bronchoscopy. We have demonstrated that MRI data can be used to create a 3D model of the respiratory tract in a normal fetus. We believe that this technique could become a useful tool for the assessment of fetal airway patency.

Interactive microbial genome visualization with GView

Summary: GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications.Availability: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.caContact: gary.van.domselaar@phac-aspc.gc.ca

JSBML

AbstractThe XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.

JSBML

The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.

LibSBGN: Electronic Processing of SBGN maps

AbstractIntroduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations. Results To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.

Airborne data processing and analysis software package

The practice of conducting quality control and quality assurance in the construction of data sets is often an overlooked and underestimated task of many research projects in the Earth Sciences. The development of software to effectively process and quickly analyze measurements is a critical aspect of a research project. An evolutionary approach has been used at the University of North Dakota to develop and implement software to process and analyze airborne measurements. Development over the past eight years has resulted in a collection of software named the Airborne Data Processing and Analysis (ADPAA) package which has been published as an open source project on Source Forge. The ADPAA package is intended to fully automate data processing while incorporating the concept of missing value codes and levels of data processing. At each data level, ADPAA utilizes a standard ASCII file format to store measurements from individual instruments into separate files. After all data levels have been processed, a summary file containing parameters of scientific interest for the field project is created for each aircraft flight. All project information is organized into a standard directory structure. ADPAA contains several tools that facilitate quality control procedures conducted on instruments during field projects and laboratory testing. Each quality control procedure is designed to ensure proper instrument performance and hence the validity of the instrument’s measurement. Data processing by ADPAA allows edit files to be created that are automatically used to insert missing value codes into a time period that had instrument problems. The creation of edit files is typically done after the completion of a field project when scientists are performing quality assurance of the data set. Since data processing is automatic, preliminary data can be created and analyzed within hours of an aircraft flight and a complete field project data set can be reprocessed many times during the quality assurance process. Once a final data set has been created, ADPAA provides several tools for visualization and analysis. In addition to aircraft data, ADPAA can be used on any data set that is based on time series measurements. The concepts illustrated by ADPAA and components of ADPAA, such as the Cplot visualization tool, are applicable to areas of Earth Science that work with time series measurements.

Preliminary Evaluation of Baseline Relative Accuracies Using L1 Frequency Observations of Navigation-Grade GARMIN Receivers

Handheld navigation global positioning system (GPS) receivers are significantly cheaper and their position determination accuracy is less than their geodetic-grade counterparts. Although the main observable in most low-cost handheld GPS receivers is the coarse acquisition (C/A) code, some receive L1 frequency observations and utilize them to smooth the code measurements. In this technical paper, we examined the use of the C/A code and L1 phase observations captured by two GARMIN eTrex receivers in a postprocessing mode. We used software applications that send low level commands to download and save the receiver data stream and convert the observations into standard RINEX file format. Nineteen baselines with different lengths were observed using the eTrex receivers and dual frequency geodetic-grade receivers. The baseline lengths were derived from the eTrex observations and compared to corresponding ones derived from the higher accuracy geodetic-grade receiver observations. Several tests were conducted to analyze the effect of potential error sources on the achieved accuracy. The results showed that low satellite angles and existing cycle slips contributed to the errors in the processed eTrex data. The implementation of a cycle slip detection algorithm and their subsequent deletion significantly enhanced the obtained baseline relative accuracy to a finally limited range of 1.8–13.4 cm/km.

XML-based neutral file and PLM integrator for PPR information exchange between heterogeneous PLM systems

PLM (product lifecycle management) is an innovative manufacturing paradigm which allows company's engineering contents to be developed and integrated with all business processes in the extended enterprise throughout the product lifecycle. This allows engineering decisions to be made with a full understanding of the product and its portfolio, including processes, resources, and plants. For today's manufacturing industries, support from software systems is essential for the creation, management, and coordination of all manufacturing-related information. Generally, PDM (product data management) systems are extended to PLM systems to manage all PPR (product, process, resource) information throughout the product lifecycle. To implement PLM in an environment where many different information management systems are being used, an application to exchange data, files, and information between heterogeneous PLM systems is essential, and a standard file format for the exchanges is extremely desirable. In this paper, PPRX is defined as a standard data format using XML for a neutral file containing PPR information, and PLM integrator, which supports PPR information exchanges between commercial heterogeneous PLM systems and other systems is developed. With the proposed implementation and a case study for an automotive company, exchanges of PPR information can be made without loss, which reduces unnecessary effort and helps successful implementation of PLM by supporting effective integration and information sharing.