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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes [article]

Victoria Pascal Andreu, Hannah E Augustijn, Koen van den Berg, Justin J.J. van der Hooft, Michael A Fischbach, Marnix H Medema
2020 bioRxiv   pre-print
Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of metabolic gene clusters in their genomes, no automated pipelines exist to profile the  ...  Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and  ...  and automated process to 102 .  ... 
doi:10.1101/2020.12.14.422671 fatcat:n3itfwxsxfe4hb76yjomigrlra

14-1 中継マイクロ波送受信シミュレーションシステム
Super Mapping Automated Profile & Perspective System

Jun-ichi Tokimatsu, Tokuyasu Hara, Tersuo Makino, Hideo Yamamoto
1997 Proceedings of the ITE Annual Convention  
中継 マ イク ロ 波 送 受 信シミ ュ レ ー シ ョ ン シ ス テ ム 14 − 1 Super Mapping Automated Profile &Perspective $ ystem 時 松 淳 一 原 徳 康 牧野 鉄 雄 山 本 英雄 Jun − ichi Tokimatsu 丁okuyasu Hara Tetsuo Makino Hideo Yamamoto 日 本テ レ ビ放送  ...  3 .機能 概 要 ・ プ ロ フ イ ー ル プ ロ フ ィ ー ル ( Profile ) と は 中 継現 場 か ら受信 基 地 局 ま で の 距 離 と高 さ に よ る 2 次元 断 面 図 の こ と で あ る。 こ の プロ フ ィ ー ル は SMAPP SYSTEM の 要 と い え る。  ... 
doi:10.11485/iteac.1997.0_164 fatcat:did4jqgsrzacnjcptvbzpl3dzu

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

Victória Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema, Elizabeth Anne Shank
2021 mSystems  
Here, we present BiG-MAP (the Biosynthetic Gene cluster Meta'omics Abundance Profiler), which provides a streamlined and automated process to determine BGC/MGC abundance and expression in bacterial communities  ...  Altogether, this tool presents a streamlined method to functionally profile meta-omics data by mapping reads to known or putative gene clusters.  ... 
doi:10.1128/msystems.00937-21 pmid:34581602 pmcid:PMC8547482 fatcat:n3gni4klfrewxdymg6cctjoiny

プロフィール自動作成(MAPP)の開発 : 放送現業技術
Development of Mapping on Automated Profile & Perspective

Koki Tejima, Hajime Fukuyama, Kazuhiro Tuboi, Koji Kato
1988 ITE Technical Report  
ソ フ ト ウ z ア MAPP ( Mapping on Automated Profile & Perspctive ) は 次 の 独 立 し た 3 本 の ソ フ ト ウ エ ア か ら な る 。  ...  テ レ ビ ジ ョ ン 学 会 技 術 報 告 プ ロ フ ィ ー ル 自 動 作 成 ( MAPP ) の 開 発 Development of Mapping on Automated Profile & Perspective 手 島 弘 毅 福 山 肇 坪 井 和 弘 加 藤 浩 司 Tej ima K6ki Fukuyama Haj ime Tuboi I〈azuhiro Kato K6ji  ... 
doi:10.11485/tvtr.12.19_31 fatcat:ioyre64dy5ebpkjw3trnkxpkee

Automated Measurement of Hepatic Fat in T1-Mapping and DIXON MRI as a Powerful Biomarker of Metabolic Profile and Detection of Hepatic Steatosis

Khouloud AFFI, Mnaouer KACHOUT
2020 International Journal of Advanced Computer Science and Applications  
Abnormal or excessive excess of intraperitoneal fat at different anatomical sites (heart, kidneys, liver, etc.) alters the metabolic profile by generating diseases causing cardiovascular complications.  ...  Fig. 2 . 2 Diagram of the Proposed Approach to Liver Segmentation: A: Fat Map; B: Pretreatment; C: T1-Mapping;D: Classification of the Water Map Into 2 Classes; E: Background of the Image; Liver Class;  ...  They can serve as an effective and precise tool for the diagnosis and differentiation of risk profiles of patients with metabolic diseases and could be considered in the future to predict cardiovascular  ... 
doi:10.14569/ijacsa.2020.0110362 fatcat:6qlef7qvlvgopjvygagphnxvaq

Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes

Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya
1999 Genome Informatics Series  
In the final stage of the automated processing, a master spot pattern, on which all the spots in the RLGS images are mapped at once, can be obtained.  ...  enzyme recognition sites as the landmark and maps them onto a 2-D electrophoresis gel.  ...  RLGS profiles are mapped, and have developed the computer algorithm for automated MSP generation.  ... 
doi:10.11234/gi1990.10.121 fatcat:osovn3u2qfdojor5dhf3jdn67i

Bridging XML and UML - An Automated Framework

Arthur Kühlwein, Sebastian Reiter, Wolfgang Rosenstiel, Oliver Bringmann
2019 Proceedings of the 7th International Conference on Model-Driven Engineering and Software Development  
We propose an automated framework for integrating arbitrary XML data into UML models using an automatically generated UML profile corresponding to the structure of the XML data.  ...  User-defined XML-to-UML mappings further enhance this integration. Our approach mitigates the aforementioned issues while providing the same benefits.  ...  Automation As mentioned earlier, our framework is almost completely automated. The only part requiring manual effort is the specification of the user-defined mapping between XML and UML elements.  ... 
doi:10.5220/0007470403800387 dblp:conf/modelsward/Kuhlwein0R019 fatcat:axwuddxkenc5jn5dxcn5n5dyd4

Automated grain size measurements from airborne remote sensing for long profile measurements of fluvial grain sizes

Patrice E. Carbonneau, Normand Bergeron, Stuart N. Lane
2005 Water Resources Research  
This paper shows that the application area of automated grain size mapping can be extended in order to include the shallow wetted areas of the channel.  ...  2005) 'Automated grain size measurements from airborne remote sensing for long profile measurements of fluvial grain sizes.', Water resources research., 41 . W11426.  ...  Automated Long Profile Measurements [17] The resulting grain size maps can then be used to extract grain sizes in a downstream direction.  ... 
doi:10.1029/2005wr003994 fatcat:3ss2rtmq5fcunpdhzofovgizmm

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

Hanjoo Kim, Pablo Cordero, Rhiju Das, Sungroh Yoon
2013 Nucleic Acids Research  
HiTRACE has been used extensively for quantitating data from RNA and DNA structure mapping experiments, including mutate-and-map contact inference, chromatin footprinting, the EteRNA RNA design project  ...  Here we present HiTRACE-Web, an online version of HiTRACE that includes standard features previously available in the command-line version as well as additional features such as automated band annotation  ...  METHOD OVERVIEW HiTRACE-Web takes as input a set of nucleic acid structure mapping profiles obtained from a number of capillaries.  ... 
doi:10.1093/nar/gkt501 pmid:23761448 pmcid:PMC3692083 fatcat:r2njcmfrrvf4zebuv2zueum2fq

Geomorphometric landscape analysis using a semi-automated GIS-approach

Bernhard Klingseisen, Graciela Metternicht, Gernot Paulus
2008 Environmental Modelling & Software  
With a new method, slopes were further subdivided into upper, mid and lower slopes at significant breakpoints along slope profiles.  ...  This paper presents LANDFORM, a customized GIS application for semi-automated classification of landform elements, based on topographic attributes like curvature or elevation percentile.  ...  To avoid bias in the mapping of landforms, the photo-interpreter had no access to the landform map derived in the semi-automated way.  ... 
doi:10.1016/j.envsoft.2007.05.007 fatcat:vuhd47ewobgznipzvmzc24lbpq

Fully Automated Profile-based Calibration Strategy for Airborne and Terrestrial Mobile LiDAR Systems with Spinning Multi-beam Laser Units

Ravi, Habib
2020 Remote Sensing  
In this paper, we propose a fully automated profile-based strategy for the calibration of LiDAR-based MMS.  ...  LiDAR-based mobile mapping systems (MMS) are rapidly gaining popularity for a multitude of applications due to their ability to provide complete and accurate 3D point clouds for any and every scene of  ...  In this research, we propose an automated profile matching technique based on height map correlation.  ... 
doi:10.3390/rs12030401 fatcat:uhi2foqfevd3nhgqvu62lnn64q

SLIX: A Python package for fully automated evaluation of Scattered Light Imaging measurements on brain tissue

Jan Reuter, Miriam Menzel
2020 Journal of Open Source Software  
parameter maps (see Figure 2a -h) which reflect different characteristics of the SLI profiles: the average, the number of peaks, the average peak prominence, the average peak width, the distance between  ...  Every pixel in the resulting SLI image series contains a light intensity profile (SLI profile I(ϕ), cf. Figure 1b -c) which is characteristic for the brain tissue structure at this point.  ...  parameter maps (see Figure 2a -h) which reflect different characteristics of the SLI profiles: the average, the number of peaks, the average peak prominence, the average peak width, the distance between  ... 
doi:10.21105/joss.02675 fatcat:y4cfnhhmunbbdndobbc5zlo5w4

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J Stevens, Jaques Reifman
2008 BMC Bioinformatics  
The major algorithms implemented in PIPA are: (1) a profile database generation algorithm, which generates customized profile databases to predict particular protein functions, (2) an automated ontology  ...  Automated protein function prediction methods are needed to keep pace with high-throughput sequencing.  ...  Here, we present the three most important algorithms developed for PIPA: the profile generation procedure, the algorithm for the automated generation of GO mappings, and the GO-based consensus algorithm  ... 
doi:10.1186/1471-2105-9-52 pmid:18221520 pmcid:PMC2259298 fatcat:fs5vpnp655ewfkszlkuivzgzfq

Expressing Business Process Models as OWL-S Ontologies [chapter]

Muhammad Ahtisham Aslam, Sören Auer, Jun Shen, Michael Herrmann
2006 Lecture Notes in Computer Science  
The mapped OWL-S service can be used to increase flexibility and to automate BPEL based grid scenarios even further.  ...  The mapped OWL-S service can be used to increase flexibility and to automate BPEL based grid scenarios even further.  ...  We are working to produce more consistent mapping from BPEL to OWL-S to overcome the above-discussed limitations of our work.  ... 
doi:10.1007/11837862_38 fatcat:zelhztg2cjecjg2sdc7ogo32wy

Mapping clinically useful terminology to a controlled medical vocabulary

R C Barrows, J J Cimino, P D Clayton
1994 Proceedings. Symposium on Computer Applications in Medical Care  
We have mapped clinically used diagnostic terms from a legacy ambulatory care system to the separate controlled vocabulary of our central clinical information system.  ...  Output from the system after the term review process will be fed back to the target vocabulary via automated and semi-automated means to improve its clinical utility.  ...  Another program is then run on the reviewed file and it generates 3 output files: one file maps the code of each successfully matched Clinical Profile term to a MED code; another file maps each unmatched  ... 
pmid:7949922 pmcid:PMC2247832 fatcat:piiwvvu7pfhslcl3r3ajfpdydu
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