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BioXSD: the common data-exchange format for everyday bioinformatics web services

M. Kalas, P. Puntervoll, A. Joseph, E. Bartaseviciute, A. Topfer, P. Venkataraman, S. Pettifer, J. C. Bryne, J. Ison, C. Blanchet, K. Rapacki, I. Jonassen
2010 Bioinformatics  
The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and  ...  We have adapted a set of web services to use BioXSD as the input and output format, and implemented a testcase workflow.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq391 pmid:20823319 pmcid:PMC2935419 fatcat:z2dvwykkhnhvvjimg5zbw245rq

An efficient and robust parallel scheduler for bioinformatics applications in a public cloud: A bigdata approach

Leena Ammanna, Jagadeeshgowda Jagadeeshgowda, Jagadeesh Pujari
2022 Indonesian Journal of Electrical Engineering and Computer Science  
<p>In bioinformatics, genomic sequence alignment is a simple method for handling and analysing data, and it is one of the most important applications in determining the structure and function of protein  ...  a lot of computing resources.  ...  Experiments are presented to demonstrate the efficiency of the BLASTx algorithm. Through an experimental study, a comparison with Hadoop-BLAST for sequence alignment is presented.  ... 
doi:10.11591/ijeecs.v25.i2.pp1078-1086 fatcat:cp3alt77wbebbpax4hiya5fpnu

Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry

Tapan Behl, Ishnoor Kaur, Aayush Sehgal, Sukhbir Singh, Saurabh Bhatia, Ahmed Al-Harrasi, Gokhan Zengin, Elena Emilia Babes, Ciprian Brisc, Manuela Stoicescu, Mirela Marioara Toma, Cristian Sava (+1 others)
2021 International Journal of Molecular Sciences  
Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics  ...  , a personalized approach, and drug repositioning were considered together with translational medicine.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22126184 pmid:34201152 pmcid:PMC8227524 fatcat:foyvjk4asjfozhj2khewmnwf5q

Analyzing Proteomes and Protein Function Using Graphical Comparative Analysis of Tandem Mass Spectrometry Results

K. Jill McAfee, Dexter T. Duncan, Michael Assink, Andrew J. Link
2006 Molecular & Cellular Proteomics  
We have developed an integrated suite of multifunctional analysis software for interpreting, comparing, and displaying these results.  ...  results given the large variety of possible experimental aims.  ...  BIG-CAT facilitates rigorous and sophisticated analysis of tandem mass spectrometry results in a web-deployed and userfriendly environment for either local analysis or for promoting on-line collaborations  ... 
doi:10.1074/mcp.t500027-mcp200 pmid:16707483 fatcat:orqf4pvq4rfvpgczejx3kaxofy

Natural Language Processing, Electronic Health Records, and Clinical Research [chapter]

Feifan Liu, Chunhua Weng, Hong Yu
2012 Health Informatics Series  
A big barrier to this goal is that much of the information in EHR is still narrative.  ...  A big barrier to this goal is that much of the information in EHR is still narrative.  ...  Unlocking discrete data elements from such narrative information is a big challenge for reusing EHR data for clinical research.  ... 
doi:10.1007/978-1-84882-448-5_16 fatcat:qz5jc3lgunf5rbukasurbbn4oq

XML, bioinformatics and data integration

F. Achard, G. Vaysseix, E. Barillot
2001 Bioinformatics  
Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably  ...  Data outputs of analysis programs are another important source of information in bioinformatics.  ...  CORBA also offers a variety of services such as yellow pages, lifecycle, trading . . . .  ... 
doi:10.1093/bioinformatics/17.2.115 pmid:11238067 fatcat:b66b722fy5b4rl3tvvwsnojiui

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica per la Biodiversità Molecolare  ...  are partially supported by the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions, and by the cooperative programme 2010-2012 between the National Research Council of  ...  of new biomedical knowledge in the Big Data era.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Visual programming for next-generation sequencing data analytics

Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
2016 BioData Mining  
Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between  ...  Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone.  ...  Five years later, analysis is no longer paralyzed. A plethora of NGS data analysis software has emerged, with considerable redundancy.  ... 
doi:10.1186/s13040-016-0095-3 pmid:27127540 pmcid:PMC4848821 fatcat:tvbjlx36hbgblb5x5dl7tah6fe

Serdica Journal of Computing MANAGEABLE WORKFLOWS FOR PROCESSING PARALLEL SEQUENCING DATA

Bulgarian Academy, Milko Krachunov, Ognyan Kulev, Valeriya Simeonova, Maria Nisheva, Dimitar Vassilev
2014 ACM Computing Classification System   unpublished
Data analysis after parallel sequencing is a process that uses combinations of software tools that is often subject to experimentation and on-the-fly substitution, with the necessary file conversion.  ...  The execution system design provides user-defined operations and interchangeability between an operation and a workflow.  ...  The common data that is subject to analysis in genomics and related studies are DNA sequences and fragments, as well as aminoacid sequences and fragments.  ... 
fatcat:mvbyeyxklbakfmv7qigwcjdypy

International hearing protector standardization

Torben Poulsen
2002 Journal of the Acoustical Society of America  
The elastic properties of the U30 stones are being measured which will alow a quantitative analysis of crack growth to be performed and compared to the experimental data. ͓  ...  This study presents experimental S-I results for a thin, simply supported, rectangular plate with an attached damper excited by a diffuse acoustic field.  ...  A provision is made in the header of the file to store details of the sensor and processing for the data ͑e.g., the number of hydrophones, beam direction, FFT size͒ so that an analysis system does not  ... 
doi:10.1121/1.4779221 fatcat:gxv33fedmrhxlf35odaqh3jybm

14th International Symposium on Mathematical Programming

1990 Mathematical programming  
If we use a decomposition approach in order to solve a minimization problem we often get an objective function in such a w a y that its domain dom 6 = n is not given explicitely to us.  ...  A v ariation of bundle methods is presented by means of which such a t ype of problems can be solved.In this variation a dynamic polyhedral model of dom is generated by means of normal vectors.In addition  ...  services -www This lecture presents the software system Progress, which facilitates in an easy way the provision, usage, and combination of algorithms, data, and models via various Internet services,  ... 
doi:10.1007/bf01580875 fatcat:3jtclwmntzgjxkqs5uecombdaa

Negative Factor

Xiaochun Yang, Tao Qiu, Bin Wang, Baihua Zheng, Yaoshu Wang, Chen Li
2016 ACM Transactions on Database Systems  
We conducted a thorough experimental study of this technique on real datasets, including DNA sequences, proteins, and text documents, and show significant performance improvement of the state-of-theart  ...  The problem of finding matches of a regular expression (RE) on a string exists in many applications, such as text editing, biosequence search, and shell commands.  ...  ACKNOWLEDGMENTS The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the quality of this article.  ... 
doi:10.1145/2847525 fatcat:hxax2cvwmfbvbl4jqnxf5cbyai

Computer-aided research in natural sciences

Iris Emanuela Studeny
2010 unpublished
Main topics are the propagation of knowledge by the Internet, politics, portals, search engines and digital reconstruction of organisms.  ...  PDBe Analysis The PDBe Analysis is a service for academic and statistical analysis of the PDBe macromolecular structure database.  ...  This is a quite practical way to study the appearance of it and it is a quite impractical way to study real organisms.  ... 
doi:10.25365/thesis.11968 fatcat:624l6n3vaza3fmjcmkw6u4lucu

Sabkha [chapter]

2008 Encyclopedia of Earth Sciences Series  
Thus, an analysis of Na, Ca, Mg permits a prediction of the alkalinization hazard.  ...  Detailed analysis and data reduction can be performed to evaluate new models of soil-wheel or soil-machine interactions, especially soil compaction models and trafficability studies.  ...  Cross-reference SUSTAINABLE AGRICULTURE In theory, an agriculture that leaves an agroecosystem completely functional after a harvest, and able to sustain a succession of harvests indefinitely.  ... 
doi:10.1007/978-1-4020-3995-9_495 fatcat:56c5y4pybzggfcqfy66kzmke2u

Soil mineralogy [chapter]

Raj K. Gupta, I. P. Abrol, Charles W. Finkl, M. B. Kirkham, Marta Camps Arbestain, Felipe Macías, Ward Chesworth, James J. Germida, Richard H. Loeppert, Maurice G. Cook, G. O. Schwab, Krystyna Konstankiewicz (+8 others)
2008 Encyclopedia of Earth Sciences Series  
Thus, an analysis of Na, Ca, Mg permits a prediction of the alkalinization hazard.  ...  Detailed analysis and data reduction can be performed to evaluate new models of soil-wheel or soil-machine interactions, especially soil compaction models and trafficability studies.  ...  Cross-reference SUSTAINABLE AGRICULTURE In theory, an agriculture that leaves an agroecosystem completely functional after a harvest, and able to sustain a succession of harvests indefinitely.  ... 
doi:10.1007/978-1-4020-3995-9_545 fatcat:elhefyvm7zg33gbhcto3k5xcfi
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