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Showing 56 open source projects for "bmc"
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TekDT BMC
Tạo USB boot cài Windows tự động dựa trên Ventoy
TekDT BMC là công cụ tạo thiết bị có thể chứa nhiều bộ cài hệ điều hành, tương thích với nhiều loại máy tính có cấu hình khác nhau và quá trình cài đặt hệ điều hành diễn ra một cách tự động. Phần mềm tạo USB boot tương thích với nhiều cấu hình máy tính khác nhau, tích hợp cài đặt phần mềm tự động sau khi cài đặt Windows. -
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...Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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TekDT AIS
TekDT AIS là công cụ cài đặt các phần mềm khác
TekDT AIS là công cụ cài đặt các phần mềm khác hàng loạt một cách tự động, hỗ trợ chế độ dòng lệnh. -
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BIGSdb
Software for storing and analysing bacterial sequence data
...The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there. -
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PLEKv2
PLEKv2: predicting lncRNAs and mRNAs
...decompress Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 USAGE Python PLEK2.py -i fasta_file -m model(ve: vertebrate , pl: plant) Examples: $ python PLEK2.py -i test.fasta -m ve Aimin Li, Haotian Zhou, Siqi Xiong, Junhuai Li, Saurav Mallik, Rong Fei, Yajun Liu, Hongfang Zhou, Xiaofan Wang, Xinhong Hei, Lei Wang. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024, 25(1):756. https://doi.org/10.1186/s12864-024-10662-y -
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PLEK
predictor of long non-coding RNAs and mRNAs based on k-mer scheme
....: https://doi.org/10.1186/s12864-024-10662-y Aimin Li, Haotian Zhou, Siqi Xiong, et al. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024, 25(1):756. -
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TomoJ
ImageJ plugin to perform Electron Tomography
...registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
...User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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BMC
Notes on Scientific Computing for Biomechanics
This repository is a collection of lecture notes and code on scientific computing and data analysis for Biomechanics and Motor Control. -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
...Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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vipie
http://vipie.rd.tuni.fi/vipie/index.html
Open access and web based virome population profiling for multi-sample metagenomics NGS, please note that the web server has been updated to: http://vipie.rd.tuni.fi/vipie/index.html Now supporting COVID-19 User guide: http://vipie.rd.tuni.fi/vipie/doc/vipie_user_guide.pdf Open access: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3721-7 Please cite: Lin, J., Kramna, L., Autio, R. et al. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics 18, 378 (2017). https://doi.org/10.1186/s12864-017-3721-7 -
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LMAP_S
Lightweight Multigene Alignment and Phylogeny eStimation
Emanuel Maldonado and Agostinho Antunes (2019) LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinformatics, 20:739. doi: https://doi.org/10.1186/s12859-019-3292-5 -
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ARSystem plugins for Pentaho Kettle
AR-System step and db plugins for Pentaho Data Integration Kettle V5
Allows you to write per API to AR-System Server (BMC Remedy Action Request System). Includes two step output, one step input and one database plugin. The step plugins need the database plugin. -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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ARACNe-AP
Network Reverse Engineering through AP inference of Mutual Information
ARACNe-AP (Algorithm for the Reconstruction of Accurate Cellular Networks with Adaptive Partitioning) is a complete overhaul of the first ARACNe implementation, originally published by Margolin and colleagues in BMC Bioinformatics in 2006. -
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isiKnock
In silico knockouts for signaling pathways
...Hannig et al. (2019) isiKnock: in silico knockouts in signaling pathways, Bioinformatics, 35(5), 892–894 Amstein et al. (2017) Manatee invariants reveal functional pathways in signaling networks. BMC systems biology, 11(1), 72. Scheidel et al. (2016) In silico knockout studies of xenophagic capturing of Salmonella. PLoS computational biology, 12(12), e1005200. -
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LMAP
Lightweight Multigene Analyses in PAML
Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: https://doi.org/10.1186/s12859-016-1204-5 -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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AmpliMethProfiler
CpG methylation analysis of amplicons from bisulfite sequencing
...It can be run on Linux and OS X platforms. HOW TO CITE US: "ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons". Scala G., et al. BMC Bioinformatics (2016) 17:484, DOI: 10.1186/s12859-016-1380-3 -
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EXCAVATOR2tool
Enhanced tool for detecting CNVs from whole-exome sequencing data
ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!! We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. ... -
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Pathway-PDT
Pathway-PDT: A Flexible Pathway Analysis Tool for Nuclear Families
...Contact: rchung@nhri.org.tw Citation: Yo Son Park, Michael Schmidt, Eden R. Martin, Margaret A. Pericak-Vance and Ren-Hua Chung (2013), Pathway-PDT: a flexible pathway analysis tool for nuclear families, BMC Bioinformatics, 14:267 -
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BayesRate
Bayesian estimation of diversification rates
...The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175. -
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Tarantoga
Lightweight Event Management System (for Monitoring-Events and more)
Tarantoga is an open source lightweight event management system for events from monitoring and more, with similar functionality to IBM Tivoli TEC, Master Cell, or BMC BEM. It supports your ITIL/ITSM event management process. It relies on MongoDB to store the events and Perl as rule programming language. GUI and backend are seperate tools that communicate only via the MongoDB. Tarantoga understands EIF, so you can send events with "postemsg", "msend -e", and the tarantoga tool tsend. Via EIF, you can also connect other element managers, or TSM or .... ... -
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...Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. BMC Genomics 2014 15:858.
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The"Amip" GUI is intended to provide code examples of the methods proposed in: "Unsupervised image segmentation for microarray spots with irregular contours and inner holes" authors: Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch and Ovidiu Balacescu Journal: BMC Bioinformatics, 2015, 16:412 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0842-3 PDE were used for grid alignment, whereas autocorrelation driven PDE and k-means clustering were used for spot segmentation. The proposed segmentation procedure yields the spots median intensity values for the microarray images recorded from Cy3 and Cy5 fluorescent dyes. ...
