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TRAPLINE specifications

Information


Unique identifier OMICS_10971
Name TRAPLINE
Alternative name Transparent Reproducible and Automated PipeLINE
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input format FASTQ
Biological technology Illumina, Life Technologies
Parallelization MapReduce
Computer skills Basic
Stability Stable
High performance computing Yes
Maintained Yes

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Maintainer


  • person_outline Olaf Wolkenhauer <>

Publication for Transparent Reproducible and Automated PipeLINE

TRAPLINE in pipeline

2017
PMCID: 5668267
PMID: 29097735
DOI: 10.1038/s41467-017-01342-5

[…] annotation, including functional annotation clustering and functional classification, was performed with david and based on gene ontology terms. we used our openly available rna sequencing pipeline (trapline) for data analysis., weighted gene coexpression network analysis was performed by applying the r package “wgcna” to rnaseq data. we first constructed the topological overlap matrix (tom) […]


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TRAPLINE in publications

 (21)
PMCID: 5903881
PMID: 29670947
DOI: 10.1126/sciadv.aar6603

[…] (mnh). sampling effort in plots ranged from 1272 to 3828 mnh. rodents and shrews were collected using the paceline method, which consists of placing traps at 5-m intervals on transects (). on each trapline, three types of traps were used: sherman lfa traps, victor snap traps, and pitfall traps. traplines were monitored for 21 nights in each plot. species were identified using dna barcoding., […]

PMCID: 5725577
PMID: 29230062
DOI: 10.1038/s41598-017-17553-1

[…] reduce the search space, allowing rapid adoption of efficient routes., central place foragers, like bees, that visit multiple feeding destinations on a single foraging trip, often show evidence of ‘trapline’ routes, returning to the same locations in a repeatable order, like hunters checking a series of traps–. traplining ensures animals do not need to search afresh on each trip, and reduces […]

PMCID: 5668267
PMID: 29097735
DOI: 10.1038/s41467-017-01342-5

[…] annotation, including functional annotation clustering and functional classification, was performed with david and based on gene ontology terms. we used our openly available rna sequencing pipeline (trapline) for data analysis., weighted gene coexpression network analysis was performed by applying the r package “wgcna” to rnaseq data. we first constructed the topological overlap matrix (tom) […]

PMCID: 5677488
PMID: 29152186
DOI: 10.1002/ece3.3337

[…] also affects wolverine survivorship (krebs et al., ), but alberta lacks a robust measure of trap effort (webb et al., ). there is a harvest quota of one wolverine and one accidental wolverine per trapline per season (alberta fish and wildlife ); our findings suggest a conservative approach to harvest may be warranted along alberta's east slopes., our regionally comprehensive landscape data […]

PMCID: 5590137
PMID: 28882186
DOI: 10.1186/s13002-017-0180-9

[…] some parts of the region. our preliminary conversations with trappers (both indigenous and non-indigenous) have suggested intra-regional variability in the evolution of fisher and marten abundances. trapline area averages 100 km2 in abitibi-témiscamingue (minimum area = 21 km2 and maximum area = 643 km2 for 498 traplines).fig. 2 , trapping is an activity that requires knowledge of the biology […]


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TRAPLINE institution(s)
Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany; Reference und Translation Center for Cardiac Stem Cell Therapy (RTC), University of Rostock, Rostock, Germany; Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia; Gene Center Munich, LMU Munich, Munich, Germany; Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa; Sydney Medical School, University of Sydney, Sydney, NSW, Australia
TRAPLINE funding source(s)
Supported by the Federal Ministry of Education and Research Germany (FKZ 0312138A, FKZ 316159 and FKZ 02NUK043C) and the State Mecklenburg-Western Pomerania with EU Structural Funds (ESF/IV-WM-B34-0030/10 and ESF/IV-BM-B35-0010/12), by the DFG (DA 1296–1), the German Heart Foundation (F/01/12), by the FORUN Program of Rostock University Medical Centre (889001) and the EU funded CaSyM project (grant agreement #305033).

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