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The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications

BMC BIOINFORMATICS 2005年第1期6卷 21-21页

作者： Moreland, JL Gramada, A Buzko, OV Zhang, Q Bourne, PE San Diego Supercomp Ctr 9500 Gilman Dr La Jolla CA 92093 USA Univ Calif San Diego Dept Pharmacol 9500 Gilman Dr La Jolla CA 92093 USA

Background: The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web. Results: We describe a new software toolkit - the Molecular Biology Toolkit (MBT;http://***) - that enables fast development of applications for protein analysis and visualization. The toolkit is written in Java, thus offering platform-independence and Internet delivery capabilities. Several applications of the toolkit are introduced to illustrate the functionality that can be achieved. Conclusions: The MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).

关键词： Protein Data Bank application programming interface Class Hierarchy Common Data Model Sequence Viewer

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Incorporation of computational routines in a microservice architecture in AgDataBox platform

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SUSTAINABLE COMPUTING-INFORMATICS & SYSTEMS 2024年 44卷

作者： Sobjak, Ricardo de Souza, Eduardo Godoy Bazzi, Claudio Leones Schenatto, Kelyn Betzek, Nelson Miguel Gavioli, Alan Fed Univ Technol Parana UTFPR Dept Comp Sci Medianeira Parana Brazil Western Parana State Univ UNIOESTE Technol & Exact Sci Ctr PGEAGRI Cascavel Parana Brazil

Agriculture has been undergoing a digital process that aims to apply digital technologies to make the sector more productive, profitable, and environmentally responsible. This trend has been adopted since applying precision agriculture (PA) techniques and, more recently, with digital agriculture (DA). DA aims to use all available information and knowledge to enable the automation of sustainable processes in agriculture, applying data analysis methods and techniques by specific software and platforms to collect and transform data into meaningful information for agriculture. Platform AgDataBox (ADB) offers tools to allow agriculture specialists to obtain, process, and visualize data for the correct decision-making. However, its structure needed to be readjusted to new software architecture to allow the aggregation of new functionalities and expand the ADB platform. This study aimed to develop a web microservices architecture (ADB-MSA) to incorporate the required functionalities to create thematic maps (TMs) and delineate management zones (MZs). ADB-MSA provided eight microservices, six of which (statistics, spatial, interpolation, clustering, rectification, and lime/nutrient recommendation) execute procedures based on JavaScript, R, and Python programming languages. At the same time, the other two are used to store data. In the case study, the procedures to create TMs and delineate MZs were performed with data from one commercial area. Thus, the services provided in the architecture meet the steps of creating TMs and delineating MZs, as MZs for fertilizer application were generated and evaluated according to phosphorus and potassium requirements. ADB-MSA allows the development of several new client applications (web, mobile, desktop, and embedded systems) to promote solutions in agriculture, streamlining processes, as it abstracts the implementation and execution complexity of available algorithms.

关键词： Precision agriculture Digital agriculture Management zone Thematic map application programming interface Agricultural software

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Worst-Case Execution-Time-Aware Parallelization of Model-Based Avionics applications

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JOURNAL OF AEROSPACE INFORMATION SYSTEMS 2019年第11期16卷 521-533页

作者： Reder, Simon Kempf, Fabian Bucher, Harald Becker, Juergen Alefragis, Panayiotis Voros, Nikolaos Skalistis, Stefanos Derrien, Steven Puaut, Isabelle Oey, Oliver Stripf, Timo Ferdinand, Christian David, Clement Ulbig, Peer Mueller, David Durak, Umut Karlsruhe Inst Technol ITIV Engesserstr 5 D-76131 Karlsruhe Germany Univ Peloponnese Elect & Comp Engn Dept Megalou Alexandrou 1 Patras 26334 Greece Univ Rennes 1 IRISA Ave Gen Leclerc F-35042 Rennes France Emmtrix Technol GmbH Haid & Neu Str 7 D-76131 Karlsruhe Germany AbsInt Angew Informat GmbH Sci Pk 1 D-66123 Saarbrucken Germany ESI Grp F-75015 Paris France German Aerosp Ctr DLR Inst Flight Syst Lilienthalpl 7 D-38108 Braunschweig Germany Scilab Enterprises 143 Bis Rue Yves Le Coz F-78000 Versailles France

Multicore processing systems are the solution of choice to provide high embedded computing performance, but drawbacks in timing predictability and programmability limit their adoption in safety-critical aerospace applications. This work presents a compiler tool flow for automated parallelization of model-based real-time software, which addresses the shortcomings of multicore architectures in real-time systems. The flow is demonstrated using a model-based terrain awareness and warning systems (TAWSs) and an edge detection algorithm from the image-processing domain. Model-based applications are first transformed into real-time C code and, from there, into a well-predictable parallel C program. Tight bounds for the worst-case execution time (WCET) of the parallelized program can be determined using an integrated multicore WCET analysis. Thanks to the use of an architecture description language, the general approach is applicable to a wider range of target platforms. An experimental evaluation for a research architecture with network-on-chip interconnect shows that the parallel WCET of the TAWS application can be improved by a factor of 1.77 using the presented compiler tools.

关键词： Worst Case Execution Time Enhanced Ground Proximity Warning System High Performance Computing Real Time System Real Time Software Image Processing Model Based Design Graphical User interface application programming interface Time Division Multiple Access

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Apicula: Static detection of API calls in generic streams of bytes

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COMPUTERS & SECURITY 2022年 119卷 1页

作者： D'Onghia, Mario Salvadore, Matteo Nespoli, Benedetto Maria Carminati, Michele Polino, Mario Zanero, Stefano Dipartimento Elettron Informaz & Bioingn Milan Italy

API functions often require the crafting of specific inputs and may return some output that is usually processed by the code that immediately follows their invocation. In this work, we claim that - for some APIs - those two stages are both frequently similar across different binaries and sufficiently unique to be fingerprinted. We build upon this intuition and present Apicula , a static analysis tool for identifying API calls in generic streams of bytes, such as memory dumps, network traffic, or object code files. In a nutshell, Apicula leverages the control flow graph of a binary to generate a set of fingerprints for all basic blocks that end with a call instruction. Those sets are then compared against a database of pre-computed fingerprints to establish whether any known API is being invoked. Due to its applicability to unstructured byte streams, Apicula can complement the reverse engineering process when this is carried out over memory dumps collected after a cyber-incident. Moreover, it can enable behavioral analysis in a fully static way, by identifying sequences of API calls even in non executable binaries. We provide a series of experiments that are instrumental (1) in demonstrating that the same fingerprints computed for specific APIs can be observed across different binaries and (2) in identifying a subset of the Windows APIs whose usage can be detected by Apicula with sufficient precision and sensitivity, focusing in particular on malicious binaries . Furthermore, we illustrate two techniques that can be used to validate different fingerprint databases in case someone wants to detect APIs belonging to libraries different from those that we consider in this work. In particular, we prove that fingerprints associated with different APIs are remarkably dissimilar and therefore can be employed for distinguishing between APIs. More specifically, we find that fingerprint sets associated with different APIs present on average a Jaccard index value of 0.0 0 0125;i

关键词： application programming interface detection Binary analysis Static analysis Code fingerprinting Malware analysis

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Learning to recommend third-party library migration opportunities at the API level

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APPLIED SOFT COMPUTING 2020年 90卷 106140-000页

作者： Alrubaye, Hussein Mkaouer, Mohamed Wiem Khokhlov, Igor Reznik, Leon Ouni, Ali Mcgoff, Jason Rochester Inst Technol Rochester NY 14623 USA Univ Quebec Ecole Technol Super Quebec City PQ Canada Xerox Corp Rochester NY USA

The manual migration between different third-party libraries represents a challenge for software developers. Developers typically need to explore both libraries application programming interfaces, along with reading their documentation, in order to locate the suitable mappings between replacing and replaced methods. In this paper, we introduce RAPIM, a machine learning model that recommends mappings between methods from two different libraries. Our model learns from previous migrations, manually performed in mined software systems, and extracts a set of features related to the similarity between method signatures and method textual documentations. We evaluate our model using 8 popular migrations, collected from 57,447 open-source Java projects. Results show that RAPIM is able to recommend relevant library API mappings with an average accuracy score of 87%. Finally, we provide the community with an API recommendation web service that could be used to support the migration process. (C) 2020 Elsevier B.V. All rights reserved.

关键词： application programming interface Library migration Machine learning Software quality Mining software repositories

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Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing

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BMC BIOINFORMATICS 2004年第1期5卷 162-162页

作者： Boehm, AM Galvin, RP Sickmann, A Univ Wurzburg Rudolf Virchow Ctr Expt Biomed Prot Mass Spectrometry & Funct Proteom Grp D-97078 Wurzburg Germany Applera UK Appl Biosyst Warrington WA3 7QH Cheshire England

Background: Mass spectrometry based proteomics result in huge amounts of data that has to be processed in real time in order to efficiently feed identification algorithms and to easily integrate in automated environments. We present wiff2dta, a tool created to convert MS/MS data obtained using Applied Biosystem's QStar and QTrap 2000 and 4000 series. Results: Comparing the performance of wiff2dta with the standard tools, we find wiff2dta being the fastest solution for extracting spectrum data from ABIs raw file format. wiff2dta is at least 10% faster than the standard tools. It is also capable of batch processing and can be easily integrated in high throughput environments. The program is freely available via http://***,http://***/projects/protms/ and is also available from Applied Biosystems. Conclusions: wiff2dta offers the possibility to run as stand-alone application or within a batch process as command-line tool integrated in automation and high-throughput environments. It is more efficient than the state-of-the-art tools provided.

关键词： Graphical User interface application programming interface Binary File Command Line Option Mascot Generic Format

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Multi-Level High Precision LBS Architecture Based on GNSS CORS Network, A Case Study of HNCORS

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IEEE ACCESS 2019年 7卷 185042-185054页

作者： Sun, Hua Dong, Mingxu Chu, Bin Ao, Minsi Chen, Chunhua Gu, Shouzhou Wuhan Univ State Key Lab Informat Engn Surveying Mapping & R Wuhan 430074 Peoples R China Hunan Inst Geomat Sci & Technol HNCORS Data Ctr Changsha 410007 Peoples R China Wuhan Univ GNSS Res Ctr Wuhan 430079 Peoples R China Chinese Acad Surveying & Mapping Inst Geodesy & GNSS Nav Beijing 100083 Peoples R China

With the rapid development of the ground infrastructure as CORS and mobile communication stations, the high precision LBS expand from the limited fields to the public. The comprehensive LBS platforms which meet the demands such as multi-precision level, massive user and desirable scalability, become critical for the public applications. In this paper, a new high precision LBS architecture based on GNSS CORS network is presented. The platform is deployed in the cloud computational environment. It is divided into two parts: data processing and allocation system individually. The virtual grids differential corrections are involved to optimize the real-time CORS stations data processing. Besides, the API/SDK module is introduced as a new service mode, which integrates the meter, decimeter, centimeter level LBS applications, respectively realized by the coordinates, pseudo range and carrier phase differential. With the daily needs of HNCORS network, the platform "SoBDS" is established. The experiments for decimeter level example shows that, the platform could support one million users, and it is compatible and scalable. The real-time positioning accuracy is +/- 0.425m and +/- 0.436m in east and north. The total accuracy is +/- 0.612m and +/- 0.773m in horizontal and vertical direction.

关键词： Global positioning system global navigation satellite system continuously operating reference stations location based service platform RTCM protocol application programming interface software development kit

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ErmineJ: Tool for functional analysis of gene expression data sets

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BMC BIOINFORMATICS 2005年第1期6卷 269-269页

作者： Lee, HK Braynen, W Keshav, K Pavlidis, P Columbia Univ Columbia Genome Ctr New York NY 10032 USA Columbia Univ Dept Comp Sci New York NY 10025 USA Univ Arizona Dept Philosophy Tucson AZ 85721 USA

Background: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. Results: We introduce ErmineJ, a multiplatform user-friendly stand- alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. Conclusion: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://***.

关键词： Gene Ontology application programming interface Annotation File Gene Score Command Line interface

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kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes

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BMC BIOINFORMATICS 2023年第1期24卷 78-78页

作者： Huckvale, Erik Moseley, Hunter N. B. Univ Kentucky Markey Canc Ctr Lexington KY 40536 USA Univ Kentucky Dept Mol & Cellular Biochem Lexington KY 40536 USA Univ Kentucky Inst Biomed Informat Lexington KY 40536 USA

BackgroundThe Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and reusable (FAIR) by providing RESTful access to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software package support available in a given programming language. While R library support for KEGG is fairly strong, Python library support has been lacking. Moreover, there is no software that provides extensive command line level support for KEGG access and *** present kegg_pull, a package implemented in the Python programming language that provides better KEGG access and utilization functionality than previous libraries and software packages. Not only does kegg_pull include an application programming interface (API) for Python programming, it also provides a command line interface (CLI) that enables utilization of KEGG for a wide range of shell scripting and data analysis pipeline use-cases. As kegg_pull's name implies, both the API and CLI provide versatile options for pulling (downloading and saving) an arbitrary (user defined) number of database entries from the KEGG API. Moreover, this functionality is implemented to efficiently utilize multiple central processing unit cores as demonstrated in several performance tests. Many options are provided to optimize fault-tolerant performance across a single or multiple processes, with recommendations provided based on extensive testing and practical network *** new kegg_pull package enables new flexible KEGG retrieval use cases not available in previous software packages. The most notable new feature that kegg_pull provides is its ability to robustly pull an arbitrary number o

关键词： KEGG REST application programming interface Python programming language Command line interface

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A high-level 3D visualization API for Java and ImageJ

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BMC BIOINFORMATICS 2010年第1期11卷 274-274页

作者： Schmid, Benjamin Schindelin, Johannes Cardona, Albert Longair, Martin Heisenberg, Martin Univ Wurzburg Dept Neurobiol & Genet Bioctr Wurzburg Germany Max Planck Inst Mol Cell Biol & Genet Dresden Germany Uni ETH Zurich Inst Neuroinformat Zurich Switzerland Univ Edinburgh Sch Informat Edinburgh Midlothian Scotland

Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://***.

关键词： Image Volume application programming interface Volume Rendering Scene Graph Volume Editing

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