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1.  DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells 
Immunome Research  2010;6:10.
Background
The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs).
Results
Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules.
Conclusions
The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies.
doi:10.1186/1745-7580-6-10
PMCID: PMC3000836  PMID: 21092113
2.  Software support for SBGN maps: SBGN-ML and LibSBGN 
Bioinformatics  2012;28(15):2016-2021.
Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.
Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net.
Contact: sbgn-libsbgn@lists.sourceforge.net
doi:10.1093/bioinformatics/bts270
PMCID: PMC3400951  PMID: 22581176
3.  Editing, validating and translating of SBGN maps 
Bioinformatics  2010;26(18):2340-2341.
Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable.
Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats.
Availability: SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files.
Contact: schreibe@ipk-gatersleben.de
doi:10.1093/bioinformatics/btq407
PMCID: PMC2935428  PMID: 20628075
4.  CySBGN: A Cytoscape plug-in to integrate SBGN maps 
BMC Bioinformatics  2013;14:17.
Background
A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.
Results
We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network.
Conclusions
CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.
doi:10.1186/1471-2105-14-17
PMCID: PMC3599859  PMID: 23324051
5.  BioPAX support in CellDesigner 
Bioinformatics  2011;27(24):3437-3438.
Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.
Availability: The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/
Contact: huaiyumi@usc.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr586
PMCID: PMC3232372  PMID: 22021903
6.  Payao: a community platform for SBML pathway model curation 
Bioinformatics  2010;26(10):1381-1383.
Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members.
Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported.
Contact: kitano@sbi.jp
doi:10.1093/bioinformatics/btq143
PMCID: PMC2865864  PMID: 20371497
7.  FNV: light-weight flash-based network and pathway viewer 
Bioinformatics  2011;27(8):1181-1182.
Motivation: Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways.
Summary: Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials.
Availability: FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV.
Contact: avi.maayan@mssm.edu
doi:10.1093/bioinformatics/btr098
PMCID: PMC3072557  PMID: 21349871
8.  LibSBML: An API Library for SBML 
Bioinformatics (Oxford, England)  2008;24(6):880-881.
Summary
LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation, and validation software.
Availability
LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml.
Contact
sbml-team@caltech.edu
doi:10.1093/bioinformatics/btn051
PMCID: PMC2517632  PMID: 18252737
9.  A comprehensive map of the mTOR signaling network 
The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation. mTOR signaling is frequently dysregulated in oncogenic cells, and thus an attractive target for anticancer therapy. Using CellDesigner, a modeling support software for graphical notation, we present herein a comprehensive map of the mTOR signaling network, which includes 964 species connected by 777 reactions. The map complies with both the systems biology markup language (SBML) and graphical notation (SBGN) for computational analysis and graphical representation, respectively. As captured in the mTOR map, we review and discuss our current understanding of the mTOR signaling network and highlight the impact of mTOR feedback and crosstalk regulations on drug-based cancer therapy. This map is available on the Payao platform, a Web 2.0 based community-wide interactive process for creating more accurate and information-rich databases. Thus, this comprehensive map of the mTOR network will serve as a tool to facilitate systems-level study of up-to-date mTOR network components and signaling events toward the discovery of novel regulatory processes and therapeutic strategies for cancer.
doi:10.1038/msb.2010.108
PMCID: PMC3018167  PMID: 21179025
cancer; CellDesigner; graphical notation; mTOR; regulatory network
10.  Kinetic Modeling using BioPAX ontology 
Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format).
doi:10.1109/BIBM.2007.55
PMCID: PMC2941992  PMID: 20862270
11.  Use of the Extensible Stylesheet Language (XSL) for medical data transformation. 
Recently, the Extensible Markup Language (XML) has received growing attention as a simple but flexible mechanism to represent medical data. As XML-based markups become more common there will be an increasing need to transform data stored in one XML markup into another markup. The Extensible Stylesheet Language (XSL) is a stylesheet language for XML. Development of a new mammography reporting system created a need to convert XML output from the MEDLee natural language processing system into a format suitable for cross-patient reporting. This paper examines the capability of XSL as a rule specification language that supports the medical XML data transformation. A set of nine relevant transformations was identified: Filtering, Substitution, Specification, Aggregation, Merging, Splitting, Transposition, Push-down and Pull-up. XSL-based methods for implementing these transformations are presented. The strengths and limitations of XSL are discussed in the context of XML medical data transformation.
PMCID: PMC2232783  PMID: 10566337
12.  From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language 
Background
Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization.
Results
The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro.
Conclusions
The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.
doi:10.1186/1758-2946-5-25
PMCID: PMC3764975  PMID: 23705910
Chemical Markup Language; FoX; NWChem; Avogadro; Computational chemistry
13.  A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway 
Biochemical Pharmacology  2013;86(1):56-66.
Graphical abstract
We present the pathways leading to cholesterol, epoxy-cholesterol and oxysterol synthesis.
Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. A detailed, integrative single-view description of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking in the existing literature. Here we provide a systematic review of the existing literature and present a detailed pathway diagram that describes the cholesterol biosynthesis pathway (the mevalonate, the Kandutch-Russell and the Bloch pathway) and shunt pathway that leads to 24(S),25-epoxycholesterol synthesis. The diagram has been produced using the Systems Biology Graphical Notation (SBGN) and is available in the SBGN-ML format, a human readable and machine semantically parsable open community file format.
doi:10.1016/j.bcp.2013.03.021
PMCID: PMC3912678  PMID: 23583456
Cholesterol; Sterol; SBGN; Metabolic network; Pathway map
14.  SBML2LaTEX: Conversion of SBML files into human-readable reports 
Bioinformatics  2009;25(11):1455-1456.
Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization.
Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX.
Contact:andreas.draeger@uni-tuebingen.de
Supplementary information:Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp170
PMCID: PMC2682517  PMID: 19307240
15.  Biographer: web-based editing and rendering of SBGN compliant biochemical networks 
Bioinformatics  2013;29(11):1467-1468.
Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner.
Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats.
Availability: The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL.
Contact: edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de
doi:10.1093/bioinformatics/btt159
PMCID: PMC3661053  PMID: 23574737
16.  Development of Clinical Contents Model Markup Language for Electronic Health Records 
Healthcare Informatics Research  2012;18(3):171-177.
Objectives
To develop dedicated markup language for clinical contents models (CCM) to facilitate the active use of CCM in electronic health record systems.
Methods
Based on analysis of the structure and characteristics of CCM in the clinical domain, we designed extensible markup language (XML) based CCM markup language (CCML) schema manually.
Results
CCML faithfully reflects CCM in both the syntactic and semantic aspects. As this language is based on XML, it can be expressed and processed in computer systems and can be used in a technology-neutral way.
Conclusions
CCML has the following strengths: it is machine-readable and highly human-readable, it does not require a dedicated parser, and it can be applied for existing electronic health record systems.
doi:10.4258/hir.2012.18.3.171
PMCID: PMC3483474  PMID: 23115739
Clinical Information System; XML; Semantics
17.  Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology 
Bioinformatics  2012;29(3):404-406.
Summary: Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported.
Availability: The software package including source code, help documentation and demonstrations are available at http://sourceforge.net/projects/gnatmatlab/files/.
Contact: neel@buffalo.edu or gangliu@buffalo.edu
doi:10.1093/bioinformatics/bts703
PMCID: PMC3562062  PMID: 23230149
18.  Development of a Google-Based Search Engine for Data Mining Radiology Reports 
The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google’s XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like “pneumothorax” yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like “hemangioendothelioma” yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google’s interface, radiologists can quickly perform useful searches.
doi:10.1007/s10278-008-9110-7
PMCID: PMC3043709  PMID: 18392657
Google; data mining; reports; HIPAA; search engine
19.  Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis 
The FASEB Journal  2013;27(7):2536-2541.
Does PubMed Central—a government-run digital archive of biomedical articles—compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.—Davis, P. M. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis.
doi:10.1096/fj.13-229922
PMCID: PMC3688741  PMID: 23554455
digital repositories; downloads; open access; scientific publishing
20.  IDR: the ImmunoDeficiency Resource 
Nucleic Acids Research  2002;30(1):232-234.
The ImmunoDeficiency Resource (IDR), freely available at http://www.uta.fi/imt/bioinfo/idr/, is a comprehensive knowledge base on immunodeficiencies. It is designed for different user groups such as researchers, physicians and nurses as well as patients and their families and the general public. Information on immunodeficiencies is stored as fact files, which are disease- and gene-based information resources. We have developed an inherited disease markup language (IDML) data model, which is designed for storing disease- and gene-specific data in extensible markup language (XML) format. The fact files written by the IDML can be used to present data in different contexts and platforms. All the information in the IDR is validated by expert curators.
PMCID: PMC99120  PMID: 11752302
21.  Qualitative translation of relations from BioPAX to SBML qual 
Bioinformatics  2012;28(20):2648-2653.
Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. With the SBML qualitative models extension (qual), it has recently also become possible to describe relations in SBML. Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations.
Results: The entire nature pathway interaction database has been converted from BioPAX (Level 2 and Level 3) into SBML (Level 3 Version 1) including both reactions and relations by using the new qual extension package. Additionally, we present the new webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared with previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact.
Availability: BioPAX2SBML is freely available at http://webservices.cs.uni-tuebingen.de/ and the complete collection of the PID models is available at http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/.
Contact: finja.buechel@uni-tuebingen.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts508
PMCID: PMC3467751  PMID: 22923304
22.  IML: An image markup language. 
Image Markup Language is an extensible markup language (XML) schema used to describe both image metadata and annotations. It describes both data pertaining to an entire image, and data that are tied to specific regions or features of the image. Developed for a specific domain in Medical Education, this pa-per describes extensions to take advantage of the Dublin Core metadata standard, and of an XML schema for vector graphics representation. We have developed a prototype system of open source tools implementing an authoring system, a client system, and an image annotation database which can be queried though the Web.
PMCID: PMC2243617  PMID: 11825219
23.  The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways 
BMC Systems Biology  2010;4:65.
Background
There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do this is currently the subject of some debate.
Results
The modified Edinburgh Pathway Notation (mEPN) scheme is founded on a notation system originally devised a number of years ago and through use has now been refined extensively. This process has been primarily driven by the author's attempts to produce process diagrams for a diverse range of biological pathways, particularly with respect to immune signaling in mammals. Here we provide a specification of the mEPN notation, its symbols, rules for its use and a comparison to the proposed Systems Biology Graphical Notation (SBGN) scheme.
Conclusions
We hope this work will contribute to the on-going community effort to develop a standard for depicting pathways and will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.
doi:10.1186/1752-0509-4-65
PMCID: PMC2878301  PMID: 20478018
24.  JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases 
BMC Bioinformatics  2005;6:47.
Background
Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language.
Results
We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture.
Conclusion
We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.
doi:10.1186/1471-2105-6-47
PMCID: PMC555758  PMID: 15757508
25.  BioJava: an open-source framework for bioinformatics in 2012 
Bioinformatics  2012;28(20):2693-2695.
Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.
Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.
Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists
Contact: andreas.prlic@gmail.com
doi:10.1093/bioinformatics/bts494
PMCID: PMC3467744  PMID: 22877863

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