Journal:From command-line bioinformatics to bioGUI - Revision history

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			==Discussion==
			bioGUI is a framework for easy GUI-based usage of CL applications in the life sciences. Using bioGUI, high-quality CL applications can be made accessible to as many researchers as possible. This is achieved by lowering the hurdles to overcome for using bioinformatics applications, particularly on Windows.

			===Use-case analysis===
			Our use-case analysis (Appendix section “Use cases”) has revealed several requirements for bioGUI (see the section “Methods”) to enable the user to perform the sequencing analysis and to allow the developer to rapidly create a template (Fig. 2).


			[[File:Fig2 Joppich PeerJ2019 7.jpg\|900px]]
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			\| style="background-color:white; padding-left:10px; padding-right:10px;"\| <blockquote>'''Figure 2.''' bioGUI use-case study, from a developer’s and user’s perspective, performed on an exemplary RNAseq analysis workflow. The dark-gray underlayed tasks represent the developer’s tasks, and the bright-yellow part represents the analysis pipeline the user wants to execute. Tasks requiring user-action are shown as rectangles and intermediate results are shown in ellipses. Cyan ellipses denote solutions/results (e.g., template repository) offered by bioGUI. bioGUI starts sub-processes for each task, such that the overhead for any started processes is as small as possible. Upon finishing a task or pipeline, bioGUI can display a notification and open generated output.</blockquote>
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	===Benchmarking bioGUI templates===		===Benchmarking bioGUI templates===
	Our benchmark comprises of four tasks. The first task is to assemble a bacterial genome from Oxford Nanopore long reads, for which the minimap2<ref name="LiMini18">{{cite journal \|title=Minimap2: pairwise alignment for nucleotide sequences \|journal=Bioinformatics \|author=Li, H. \|volume=34 \|issue=18 \|pages=3094–100 \|year=2018 \|doi=10.1093/bioinformatics/bty191 \|pmid=29750242 \|pmc=PMC6137996}}</ref>/miniasm<ref name="LiMini16">{{cite journal \|title=Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences \|journal=Bioinformatics \|author=Li, H. \|volume=32 \|issue=14 \|pages=2103–10 \|year=2016 \|doi=10.1093/bioinformatics/btw152 \|pmid=27153593 \|pmc=PMC4937194}}</ref>/racon<ref name="VaserFast17">{{cite journal \|title=Fast and accurate de novo genome assembly from long uncorrected reads \|journal=Genome Research \|author=Vaser, R.; Sović, I.; Nagarajan, N. et al. \|volume=27 \|issue=5 \|pages=737-46 \|year=2017 \|doi=10.1101/gr.214270.116 \|pmid=28100585 \|pmc=PMC5411768}}</ref> pipeline (available as install module from bioGUI) is used. The second task is the quantification of reads from a yeast mRNA sequencing project using Oxford Nanpore Reads and Illumina Reads (EMBL ENA studies PRJNA398797 [MinION] and SAMN00849440 [Illumina]). The quantification is performed using featureCounts from the subread package.<ref name="LiaoFeature14" /> The third task uses these results to compute differential gene expression. Differential gene expression analysis is performed using MS-EmpiRe in R (install module available<ref name="AmmarMS-EmpiRe19" />). Finally the fourth task uses RNAhybrid<ref name="RehmsmeierFast04" /> to predict miRNA binding sites (1,978 murine miRNAs) in 170 sequences of each 200 nt.		Our benchmark comprises of four tasks. The first task is to assemble a bacterial genome from Oxford Nanopore long reads, for which the minimap2<ref name="LiMini18">{{cite journal \|title=Minimap2: pairwise alignment for nucleotide sequences \|journal=Bioinformatics \|author=Li, H. \|volume=34 \|issue=18 \|pages=3094–100 \|year=2018 \|doi=10.1093/bioinformatics/bty191 \|pmid=29750242 \|pmc=PMC6137996}}</ref>/miniasm<ref name="LiMini16">{{cite journal \|title=Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences \|journal=Bioinformatics \|author=Li, H. \|volume=32 \|issue=14 \|pages=2103–10 \|year=2016 \|doi=10.1093/bioinformatics/btw152 \|pmid=27153593 \|pmc=PMC4937194}}</ref>/racon<ref name="VaserFast17">{{cite journal \|title=Fast and accurate de novo genome assembly from long uncorrected reads \|journal=Genome Research \|author=Vaser, R.; Sović, I.; Nagarajan, N. et al. \|volume=27 \|issue=5 \|pages=737-46 \|year=2017 \|doi=10.1101/gr.214270.116 \|pmid=28100585 \|pmc=PMC5411768}}</ref> pipeline (available as install module from bioGUI) is used. The second task is the quantification of reads from a yeast mRNA sequencing project using Oxford Nanpore Reads and Illumina Reads (EMBL ENA studies PRJNA398797 [MinION] and SAMN00849440 [Illumina]). The quantification is performed using featureCounts from the subread package.<ref name="LiaoFeature14" /> The third task uses these results to compute differential gene expression. Differential gene expression analysis is performed using MS-EmpiRe in R (install module available<ref name="AmmarMS-EmpiRe19" />). Finally the fourth task uses RNAhybrid<ref name="RehmsmeierFast04" /> to predict miRNA binding sites (1,978 murine miRNAs) in 170 sequences of each 200 nt.

			The results are shown in Table 2. The given run times are wall clock times. The peak RAM consumption has been sampled from the process viewer on the given operating systems (Task Manager on Windows, top on Linux and Mac OS).

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			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="9"\|'''Table 2.''' Benchmarking results for the four selected tasks (see Benchmarking bioGUI templates within the Results section) on the described hardware (see Table A1 in Appendix section). All runs are started via bioGUI.
			\|-
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Task
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Linux server
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Lenovo server
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Surface Book
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|MacBook Air
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|10:12 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.8 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|23:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|30:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|44:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|featureCounts (MinION)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:38 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|20 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:54 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:12 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|featureCounts (Illumina)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:13 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|28 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:41 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|02:22 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|02:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|DE quantification (MinION)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:19 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.7 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:25 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:28 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:42 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|DE quantification (Illumina)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:14 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:19 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:20 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:31 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|RNAhybrid
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|07:35 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|19 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|23:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|13:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|16:55 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\|-
			\|}
			\|}

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			===Benchmarking bioGUI templates===
			Our benchmark comprises of four tasks. The first task is to assemble a bacterial genome from Oxford Nanopore long reads, for which the minimap2<ref name="LiMini18">{{cite journal \|title=Minimap2: pairwise alignment for nucleotide sequences \|journal=Bioinformatics \|author=Li, H. \|volume=34 \|issue=18 \|pages=3094–100 \|year=2018 \|doi=10.1093/bioinformatics/bty191 \|pmid=29750242 \|pmc=PMC6137996}}</ref>/miniasm<ref name="LiMini16">{{cite journal \|title=Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences \|journal=Bioinformatics \|author=Li, H. \|volume=32 \|issue=14 \|pages=2103–10 \|year=2016 \|doi=10.1093/bioinformatics/btw152 \|pmid=27153593 \|pmc=PMC4937194}}</ref>/racon<ref name="VaserFast17">{{cite journal \|title=Fast and accurate de novo genome assembly from long uncorrected reads \|journal=Genome Research \|author=Vaser, R.; Sović, I.; Nagarajan, N. et al. \|volume=27 \|issue=5 \|pages=737-46 \|year=2017 \|doi=10.1101/gr.214270.116 \|pmid=28100585 \|pmc=PMC5411768}}</ref> pipeline (available as install module from bioGUI) is used. The second task is the quantification of reads from a yeast mRNA sequencing project using Oxford Nanpore Reads and Illumina Reads (EMBL ENA studies PRJNA398797 [MinION] and SAMN00849440 [Illumina]). The quantification is performed using featureCounts from the subread package.<ref name="LiaoFeature14" /> The third task uses these results to compute differential gene expression. Differential gene expression analysis is performed using MS-EmpiRe in R (install module available<ref name="AmmarMS-EmpiRe19" />). Finally the fourth task uses RNAhybrid<ref name="RehmsmeierFast04" /> to predict miRNA binding sites (1,978 murine miRNAs) in 170 sequences of each 200 nt.

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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install samtools-1.3.1<ref name="LiTheSeq09">{{cite journal \|title=The Sequence Alignment/Map format and SAMtools \|journal=Bioinformatics \|author=Li, H.; Handsaker, B.; Wysoker, A. et al. \|volume=25 \|issue=16 \|pages=2078-9 \|year=2009 \|doi=10.1093/bioinformatics/btp352 \|pmid=19505943 \|pmc=PMC2723002}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install SPAdes v3.13.0<ref name="BankevichSPAdes12" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (hybrid)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install StringTie v1.3.0<ref name="PerteaTranscript16" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Top Monitor (ssh example)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Technical demo
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Trimmomatic v0.36<ref name="BolgerTrimmo14" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install wtdbg2<ref name="RuanFast19" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (long-read)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Circulator<ref name="HuntCirculator15" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\|-		\|-
	\|}		\|}

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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install hisat2<ref name="KimGraph19">{{cite journal \|title=Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype \|journal=Nature Biotechnology \|author=Kim, D.; Paggi, J.M.; Park, C. et al. \|volume=37 \|issue=8 \|page=907–15 \|year=2019 \|doi=10.1038/s41587-019-0201-4 \|pmid=31375807}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install hmmer-3.1b2<ref name="WheelerNHMMER13">{{cite journal \|title=nhmmer: DNA homology search with profile HMMs \|journal=Bioinformatics \|author=Wheeler, T.J.; Eddy, S.R. \|volume=29 \|issue=19 \|page=2487-9 \|year=2013 \|doi=10.1093/bioinformatics/btt403 \|pmid=23842809 \|pmc=PMC3777106}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install jellyfish-2.2.6<ref name="MarçaisAFast11" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install minimap2/miniasm/racon (gitHub)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (long-read)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install MS-EmpiRe<ref name="AmmarMS-EmpiRe19" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install PureSeqTM<ref name="WangPure19">{{cite journal \|title=PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only \|journal=bioRxiv \|author=Wang, Q.; Ni, C.-m., Li, Z. et al. \|year=2019 \|doi=10.1101/627307}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install rMATS-3.2.5<ref name="ShenRMATS14">{{cite journal \|title=rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data \|journal=Proceedings of the National Academy of Sciences of the United States of America \|author=Shen, S.; Park, J.W.; Lu, Z.X. et al. \|volume=111 \|issue=51 \|year=2014 \|doi=10.1073/pnas.1419161111 \|pmid=25480548 \|pmc=PMC4280593}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install rnahybrid<ref name="RehmsmeierFast04">{{cite journal \|title=Fast and effective prediction of microRNA/target duplexes \|journal=RNA \|author=Rehmsmeier, M.; Steffen, P.; Hochsmann, M. et al. \|volume=10 \|issue=10 \|year=2004 \|doi=10.1261/rna.5248604 \|pmid=15383676 \|pmc=PMC4280593}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install RSEM v1.3.0<ref name="Li">{{cite journal \|title=RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome \|journal=BMC Bioinformatics \|author=Li, B.; Dewey, C.N. \|volume=12 \|year=323 \|doi=10.1186/1471-2105-12-323 \|pmid=21816040 \|pmc=PMC3163565}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|

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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install canu<ref name="KorenCanu17">{{cite journal \|title=Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation \|journal=Genome Research \|author=Koren, S.; Walenz, B.P.; Berlin, K. et al. \|volume=27 \|issue=5 \|pages=722–36 \|year=2017 \|doi=10.1101/gr.215087.116 \|pmid=28298431 \|pmc=PMC5411767}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install featureCounts<ref name="LiaoFeature14">{{cite journal \|title=featureCounts: an efficient general purpose program for assigning sequence reads to genomic features \|journal=Bioinformatics \|author=Liao, Y.; Smyth, G.K.; Shi, W. \|volume=30 \|issue=7 \|pages=923–30 \|year=2014 \|doi=10.1093/bioinformatics/btt656 \|pmid=24227677}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install glimmer302b<ref name="DelcherIdent07">{{cite journal \|title=Identifying bacterial genes and endosymbiont DNA with Glimmer \|journal=Bioinformatics \|author=Delcher, A.L.; Bratke, K.A.; Powers, E.C. et al. \|volume=23 \|issue=6 \|pages=673–9 \|year=2007 \|doi=10.1093/bioinformatics/btm009 \|pmid=17237039 \|pmc=PMC2387122}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Genome annotation
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install graphmap<ref name="SovićFast16">{{cite journal \|title=Fast and sensitive mapping of nanopore sequencing reads with GraphMap \|journal=Nature Communications \|author=Sović, I.; Šikić, M.; Wilm, A. et al. \|volume=7 \|page=11307 \|year=2016 \|doi=10.1038/ncomms11307 \|pmid=27079541 \|pmc=PMC4835549}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install albacore (pip wheel, ONT)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
	\|-		\|-
	\|}		\|}

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← Older revision		Revision as of 21:23, 6 January 2020
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	==Results==		==Results==
	===bioGUI templates===		===bioGUI templates===
			Currently more than 25 install modules exist for bioGUI. These represent basically three groups of bioinformatics tasks: next-generation sequencing data analysis and transcriptomics, long read sequencing analysis and assembly, and a more general sequence analysis. In general, these install modules will install the respective application on the local machine. The Circlator<ref name="HuntCirculator15">{{cite journal \|title=Circlator: Automated circularization of genome assemblies using long sequencing reads \|journal=Genome Biology \|author=Hunt, M.; Silva, N.D.; Otto, T.D. et al. \|volume=16 \|page=294 \|year=2015 \|doi=10.1186/s13059-015-0849-0 \|pmid=26714481 \|pmc=PMC4699355}}</ref> template allows to pull and use the corresponding Docker image. The available tools, as well as their respective categorization, are listed in Table 1.

			{\|
			\| STYLE="vertical-align:top;"\|
			{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="70%"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="4"\|'''Table 1.''' List of available templates and install modules (starting with Install) for bioGUI; tools marked with ✓ provide an install module for the operating system of the respective column.
			\|-
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Module name
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Task
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Install module
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|WSL and Ubuntu
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Mac OS
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|First Time Mac OS Setup
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Initialization
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|–
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|First Time Ubuntu/WSL/apt-get Setup
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Initialization
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|–
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Ballgown v1.0.1<ref name="PerteaTranscript16" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Bowtie1<ref name="LangmeadUltra09">{{cite journal \|title=Ultrafast and memory-efficient alignment of short DNA sequences to the human genome \|journal=Genome Biology \|author=Langmead, B.; Trapnell, C.; Pop, M. et al. \|volume=10 \|issue=3 \|page=R25 \|year=2009 \|doi=10.1186/gb-2009-10-3-r25 \|pmid=19261174 \|pmc=PMC2690996}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Bowtie2 v2.2.9<ref name="LangmeadFast12">{{cite journal \|title=Fast gapped-read alignment with Bowtie 2 \|journal=Mature Methods \|author=Langmead, B.; Salzberg, S.L. \|volume=9 \|issue=4 \|pages=357–9 \|year=2012 \|doi=10.1038/nmeth.1923 \|pmid=22388286 \|pmc=PMC3322381}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install bwa v0.7.17<ref name="LiFast09">{{cite journal \|title=Fast and accurate short read alignment with Burrows-Wheeler transform \|journal=Bioinformatics \|author=Li, H.; Durbin, R. \|volume=25 \|issue=14 \|pages=1754–60 \|year=2009 \|doi=10.1093/bioinformatics/btp324 \|pmid=19451168 \|pmc=PMC2705234}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\|}
			\|}

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← Older revision		Revision as of 21:00, 6 January 2020
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	The general workflow for any program using bioGUI is shown in Fig. 1 (above). Given a CL application, the software developer (blue) writes the specific template in an XML-based DSL and can then make this template available, for example, in the bioGUI repository (cyan). Such templates can be automatically retrieved by bioGUI. Upon selection of a template by the user, bioGUI displays the input mask as defined in the template. When the user (yellow) has filled in all parameters, the parameters are collected by bioGUI and assembled into CL arguments, which are used to execute the original CL-only application. Upon completion, simple results (like text-output or images) can be shown in bioGUI directly or within an external application that is opened.		The general workflow for any program using bioGUI is shown in Fig. 1 (above). Given a CL application, the software developer (blue) writes the specific template in an XML-based DSL and can then make this template available, for example, in the bioGUI repository (cyan). Such templates can be automatically retrieved by bioGUI. Upon selection of a template by the user, bioGUI displays the input mask as defined in the template. When the user (yellow) has filled in all parameters, the parameters are collected by bioGUI and assembled into CL arguments, which are used to execute the original CL-only application. Upon completion, simple results (like text-output or images) can be shown in bioGUI directly or within an external application that is opened.

			====Install modules====
			Install modules are designed to install applications such that bioGUI can access them. Essentially, install modules are bash scripts which allow an automatic installation of applications into a predefined location. For this purpose, install modules receive several arguments from bioGUI when launched, for example, where to install the application to, the sudo password to fetch packages via a system’s package manager (e.g., aptitude, conda), whether the application should be made available to the user via the system’s PATH variable, etc. Install modules download and install applications and make them available to the user and bioGUI. However, some applications cannot be simply downloaded, but are distributed by installers. For this purpose, the install module template can be extended by further input fields. These must be specified by bioGUI elements, and their values are added to the end of the CL arguments of the install module. An install module can then execute the referenced installer.

			Finally, an install module should contain the specification of its bioGUI template and could hardcode the path to the installed application. Other constant values, which can already be derived during the installation (e.g., absolute paths to dependencies), could also be defined in the template during this stage.

			====bioGUI templates====
			bioGUI templates are the actual end-user-interface to programs. A bioGUI template defines the look and functions of the UI. Thus it can define how the CL-application is called (with corresponding parameters).

			Each bioGUI template consists of two parts (Fig. A2). The first part (the <tt><window></tt> model) defines the visual appearance of the GUI. The second part (the <tt><execution></tt> model) defines the processing logic of the template. Input values from the GUI components are collected and assembled (e.g., pre-/post-processing steps) to call CL applications. As part of this assembly, input values from the GUI may be transformed using multiple predefined nodes. Concatenations are possible using the <tt><add></tt> node, and constant values can be inserted using the <tt><const></tt> node. System environment properties, such as the operating system, the computer’s IP address, or specific directories can be collected using the <tt><env></tt> node. If the regular nodes are not sufficient, for example, because more complex string manipulations should be made (see use-case study), script nodes may also accept functions written in [https://www.lua.org/home.html LUA] or [https://www.ecma-international.org/ecma-262/9.0/ JavaScript].

			In general, the execution part infers a network with inputs (e.g., GUI elements, other nodes within the execution part) and actions (if, add). For example, the execution network for an application with many sub-commands is exemplarily shown in Fig. A3 (see Appendix).

			The time to template varies with the application as well as the number of options to be included. A simple template, like the one for MS-EmpiRe<ref name="AmmarMS-EmpiRe19">{{cite journal \|title=MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins \|journal=Molecular and Cellular Proteomics \|author=Ammar, C.; Gruber, M.; Csaba, G. et al. \|volume=18 \|issue=9 \|pages=1880–92 \|year=2019 \|doi=10.1074/mcp.RA119.001509 \|pmid=31235637 \|pmc=PMC6731086}}</ref>, can be created within 10 minutes. More comprehensive templates, like the one for HISAT2, usually take about 30 minutes. Time can be saved if only the most important command line options are shown in the GUI. This can be achieved by adding an “optional parameters” input field, where users can insert CL arguments themselves. This is, for instance, shown in the wtdbg2<ref name="RuanFast19">{{cite journal \|title=Fast and accurate long-read assembly with wtdbg2 \|journal=Nature Methods \|author=Ruan, J.; Li, H. \|year=2019 \|doi=10.1038/s41592-019-0669-3 \|pmid=31819265}}</ref> and spades<ref name="BankevichSPAdes12">{{cite journal \|title=SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing \|journal=Journal of Computational Biology \|author=Bankevich, A.; Nurk, S.; Antipov, D. et al. \|year=2012 \|doi=10.1089/cmb.2012.0021 \|pmid=22506599 \|pmc=PMC3342519}}</ref> templates. Adding the install part to a template usually can be done within 15 to 30 minutes, depending on how detailed the build process is documented. The creation of an install module thus takes approximately one hour.

			====bioGUI integration with CWL and argparse====
			The CWL<ref name="AmstutzCommon16" /> only describes the CL workflow and neither provides a GUI nor a means to install the desired tool. Due to this more general specification, CWL fits most problems, but specific annotations of inputs, explanations, or the embedding of images is not supported in CWL.

			While developers can always create templates manually, bioGUI supports developers by offering a template generator from CWL templates or python3 argparse CL parsers. Since there are already many CWL templates available for bioinformatics CL applications, CWL files can be used as a base to automatically generate bioGUI templates from. Using the bioGUI template generator for argparse, it is also possible to automatically generate templates from CWL files (making use of the cwl2argparse program provided by CWL). Our generator takes as input the argparse parser or CWL file and creates input elements for all elements. In case the type of an input is unclear or not supported, the generator falls back to a regular text-input element.

			==Results==
			===bioGUI templates===

← Older revision		Revision as of 23:10, 6 January 2020
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	===Benchmarking bioGUI templates===		===Benchmarking bioGUI templates===
	Our benchmark comprises of four tasks. The first task is to assemble a bacterial genome from Oxford Nanopore long reads, for which the minimap2<ref name="LiMini18">{{cite journal \|title=Minimap2: pairwise alignment for nucleotide sequences \|journal=Bioinformatics \|author=Li, H. \|volume=34 \|issue=18 \|pages=3094–100 \|year=2018 \|doi=10.1093/bioinformatics/bty191 \|pmid=29750242 \|pmc=PMC6137996}}</ref>/miniasm<ref name="LiMini16">{{cite journal \|title=Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences \|journal=Bioinformatics \|author=Li, H. \|volume=32 \|issue=14 \|pages=2103–10 \|year=2016 \|doi=10.1093/bioinformatics/btw152 \|pmid=27153593 \|pmc=PMC4937194}}</ref>/racon<ref name="VaserFast17">{{cite journal \|title=Fast and accurate de novo genome assembly from long uncorrected reads \|journal=Genome Research \|author=Vaser, R.; Sović, I.; Nagarajan, N. et al. \|volume=27 \|issue=5 \|pages=737-46 \|year=2017 \|doi=10.1101/gr.214270.116 \|pmid=28100585 \|pmc=PMC5411768}}</ref> pipeline (available as install module from bioGUI) is used. The second task is the quantification of reads from a yeast mRNA sequencing project using Oxford Nanpore Reads and Illumina Reads (EMBL ENA studies PRJNA398797 [MinION] and SAMN00849440 [Illumina]). The quantification is performed using featureCounts from the subread package.<ref name="LiaoFeature14" /> The third task uses these results to compute differential gene expression. Differential gene expression analysis is performed using MS-EmpiRe in R (install module available<ref name="AmmarMS-EmpiRe19" />). Finally the fourth task uses RNAhybrid<ref name="RehmsmeierFast04" /> to predict miRNA binding sites (1,978 murine miRNAs) in 170 sequences of each 200 nt.		Our benchmark comprises of four tasks. The first task is to assemble a bacterial genome from Oxford Nanopore long reads, for which the minimap2<ref name="LiMini18">{{cite journal \|title=Minimap2: pairwise alignment for nucleotide sequences \|journal=Bioinformatics \|author=Li, H. \|volume=34 \|issue=18 \|pages=3094–100 \|year=2018 \|doi=10.1093/bioinformatics/bty191 \|pmid=29750242 \|pmc=PMC6137996}}</ref>/miniasm<ref name="LiMini16">{{cite journal \|title=Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences \|journal=Bioinformatics \|author=Li, H. \|volume=32 \|issue=14 \|pages=2103–10 \|year=2016 \|doi=10.1093/bioinformatics/btw152 \|pmid=27153593 \|pmc=PMC4937194}}</ref>/racon<ref name="VaserFast17">{{cite journal \|title=Fast and accurate de novo genome assembly from long uncorrected reads \|journal=Genome Research \|author=Vaser, R.; Sović, I.; Nagarajan, N. et al. \|volume=27 \|issue=5 \|pages=737-46 \|year=2017 \|doi=10.1101/gr.214270.116 \|pmid=28100585 \|pmc=PMC5411768}}</ref> pipeline (available as install module from bioGUI) is used. The second task is the quantification of reads from a yeast mRNA sequencing project using Oxford Nanpore Reads and Illumina Reads (EMBL ENA studies PRJNA398797 [MinION] and SAMN00849440 [Illumina]). The quantification is performed using featureCounts from the subread package.<ref name="LiaoFeature14" /> The third task uses these results to compute differential gene expression. Differential gene expression analysis is performed using MS-EmpiRe in R (install module available<ref name="AmmarMS-EmpiRe19" />). Finally the fourth task uses RNAhybrid<ref name="RehmsmeierFast04" /> to predict miRNA binding sites (1,978 murine miRNAs) in 170 sequences of each 200 nt.

			The results are shown in Table 2. The given run times are wall clock times. The peak RAM consumption has been sampled from the process viewer on the given operating systems (Task Manager on Windows, top on Linux and Mac OS).

			{\|
			\| STYLE="vertical-align:top;"\|
			{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="60%"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="9"\|'''Table 2.''' Benchmarking results for the four selected tasks (see Benchmarking bioGUI templates within the Results section) on the described hardware (see Table A1 in Appendix section). All runs are started via bioGUI.
			\|-
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Task
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Linux server
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Lenovo server
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Surface Book
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|MacBook Air
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Time
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Peak RAM
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|10:12 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.8 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|23:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|30:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|44:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|6.5 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|featureCounts (MinION)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:38 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|20 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:54 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:12 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|featureCounts (Illumina)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:13 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|28 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|01:41 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|02:22 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|02:30 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|25 MB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|DE quantification (MinION)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:19 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.7 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:25 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:28 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:42 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.6 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|DE quantification (Illumina)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:14 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.5 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:19 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:20 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|00:31 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|0.4 GB
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|RNAhybrid
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|07:35 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|19 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|23:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|13:00 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|16:55 min
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|18 MB
			\|-
			\|}
			\|}

← Older revision		Revision as of 22:41, 6 January 2020
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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install samtools-1.3.1<ref name="LiTheSeq09">{{cite journal \|title=The Sequence Alignment/Map format and SAMtools \|journal=Bioinformatics \|author=Li, H.; Handsaker, B.; Wysoker, A. et al. \|volume=25 \|issue=16 \|pages=2078-9 \|year=2009 \|doi=10.1093/bioinformatics/btp352 \|pmid=19505943 \|pmc=PMC2723002}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install SPAdes v3.13.0<ref name="BankevichSPAdes12" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (hybrid)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install StringTie v1.3.0<ref name="PerteaTranscript16" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Top Monitor (ssh example)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Technical demo
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Trimmomatic v0.36<ref name="BolgerTrimmo14" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install wtdbg2<ref name="RuanFast19" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (long-read)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Circulator<ref name="HuntCirculator15" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\|-		\|-
	\|}		\|}

← Older revision		Revision as of 22:03, 6 January 2020
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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install hisat2<ref name="KimGraph19">{{cite journal \|title=Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype \|journal=Nature Biotechnology \|author=Kim, D.; Paggi, J.M.; Park, C. et al. \|volume=37 \|issue=8 \|page=907–15 \|year=2019 \|doi=10.1038/s41587-019-0201-4 \|pmid=31375807}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install hmmer-3.1b2<ref name="WheelerNHMMER13">{{cite journal \|title=nhmmer: DNA homology search with profile HMMs \|journal=Bioinformatics \|author=Wheeler, T.J.; Eddy, S.R. \|volume=29 \|issue=19 \|page=2487-9 \|year=2013 \|doi=10.1093/bioinformatics/btt403 \|pmid=23842809 \|pmc=PMC3777106}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install jellyfish-2.2.6<ref name="MarçaisAFast11" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install minimap2/miniasm/racon (gitHub)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly (long-read)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install MS-EmpiRe<ref name="AmmarMS-EmpiRe19" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install PureSeqTM<ref name="WangPure19">{{cite journal \|title=PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only \|journal=bioRxiv \|author=Wang, Q.; Ni, C.-m., Li, Z. et al. \|year=2019 \|doi=10.1101/627307}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install rMATS-3.2.5<ref name="ShenRMATS14">{{cite journal \|title=rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data \|journal=Proceedings of the National Academy of Sciences of the United States of America \|author=Shen, S.; Park, J.W.; Lu, Z.X. et al. \|volume=111 \|issue=51 \|year=2014 \|doi=10.1073/pnas.1419161111 \|pmid=25480548 \|pmc=PMC4280593}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install rnahybrid<ref name="RehmsmeierFast04">{{cite journal \|title=Fast and effective prediction of microRNA/target duplexes \|journal=RNA \|author=Rehmsmeier, M.; Steffen, P.; Hochsmann, M. et al. \|volume=10 \|issue=10 \|year=2004 \|doi=10.1261/rna.5248604 \|pmid=15383676 \|pmc=PMC4280593}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Sequence analysis
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install RSEM v1.3.0<ref name="Li">{{cite journal \|title=RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome \|journal=BMC Bioinformatics \|author=Li, B.; Dewey, C.N. \|volume=12 \|year=323 \|doi=10.1186/1471-2105-12-323 \|pmid=21816040 \|pmc=PMC3163565}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|

← Older revision		Revision as of 21:38, 6 January 2020
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	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
	\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓		\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install canu<ref name="KorenCanu17">{{cite journal \|title=Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation \|journal=Genome Research \|author=Koren, S.; Walenz, B.P.; Berlin, K. et al. \|volume=27 \|issue=5 \|pages=722–36 \|year=2017 \|doi=10.1101/gr.215087.116 \|pmid=28298431 \|pmc=PMC5411767}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Assembly
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install featureCounts<ref name="LiaoFeature14">{{cite journal \|title=featureCounts: an efficient general purpose program for assigning sequence reads to genomic features \|journal=Bioinformatics \|author=Liao, Y.; Smyth, G.K.; Shi, W. \|volume=30 \|issue=7 \|pages=923–30 \|year=2014 \|doi=10.1093/bioinformatics/btt656 \|pmid=24227677}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install glimmer302b<ref name="DelcherIdent07">{{cite journal \|title=Identifying bacterial genes and endosymbiont DNA with Glimmer \|journal=Bioinformatics \|author=Delcher, A.L.; Bratke, K.A.; Powers, E.C. et al. \|volume=23 \|issue=6 \|pages=673–9 \|year=2007 \|doi=10.1093/bioinformatics/btm009 \|pmid=17237039 \|pmc=PMC2387122}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Genome annotation
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install graphmap<ref name="SovićFast16">{{cite journal \|title=Fast and sensitive mapping of nanopore sequencing reads with GraphMap \|journal=Nature Communications \|author=Sović, I.; Šikić, M.; Wilm, A. et al. \|volume=7 \|page=11307 \|year=2016 \|doi=10.1038/ncomms11307 \|pmid=27079541 \|pmc=PMC4835549}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install albacore (pip wheel, ONT)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install guppy (linux tar.gz, ONT)
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Long read sequencing
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
	\|-		\|-
	\|}		\|}

← Older revision		Revision as of 21:23, 6 January 2020
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	==Results==		==Results==
	===bioGUI templates===		===bioGUI templates===
			Currently more than 25 install modules exist for bioGUI. These represent basically three groups of bioinformatics tasks: next-generation sequencing data analysis and transcriptomics, long read sequencing analysis and assembly, and a more general sequence analysis. In general, these install modules will install the respective application on the local machine. The Circlator<ref name="HuntCirculator15">{{cite journal \|title=Circlator: Automated circularization of genome assemblies using long sequencing reads \|journal=Genome Biology \|author=Hunt, M.; Silva, N.D.; Otto, T.D. et al. \|volume=16 \|page=294 \|year=2015 \|doi=10.1186/s13059-015-0849-0 \|pmid=26714481 \|pmc=PMC4699355}}</ref> template allows to pull and use the corresponding Docker image. The available tools, as well as their respective categorization, are listed in Table 1.

			{\|
			\| STYLE="vertical-align:top;"\|
			{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="70%"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="4"\|'''Table 1.''' List of available templates and install modules (starting with Install) for bioGUI; tools marked with ✓ provide an install module for the operating system of the respective column.
			\|-
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Module name
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" rowspan="2"\|Task
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" colspan="2"\|Install module
			\|-
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|WSL and Ubuntu
			! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"\|Mac OS
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|First Time Mac OS Setup
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Initialization
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|–
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|First Time Ubuntu/WSL/apt-get Setup
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Initialization
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|–
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Ballgown v1.0.1<ref name="PerteaTranscript16" />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS transcriptomics
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Bowtie1<ref name="LangmeadUltra09">{{cite journal \|title=Ultrafast and memory-efficient alignment of short DNA sequences to the human genome \|journal=Genome Biology \|author=Langmead, B.; Trapnell, C.; Pop, M. et al. \|volume=10 \|issue=3 \|page=R25 \|year=2009 \|doi=10.1186/gb-2009-10-3-r25 \|pmid=19261174 \|pmc=PMC2690996}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install Bowtie2 v2.2.9<ref name="LangmeadFast12">{{cite journal \|title=Fast gapped-read alignment with Bowtie 2 \|journal=Mature Methods \|author=Langmead, B.; Salzberg, S.L. \|volume=9 \|issue=4 \|pages=357–9 \|year=2012 \|doi=10.1038/nmeth.1923 \|pmid=22388286 \|pmc=PMC3322381}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Install bwa v0.7.17<ref name="LiFast09">{{cite journal \|title=Fast and accurate short read alignment with Burrows-Wheeler transform \|journal=Bioinformatics \|author=Li, H.; Durbin, R. \|volume=25 \|issue=14 \|pages=1754–60 \|year=2009 \|doi=10.1093/bioinformatics/btp324 \|pmid=19451168 \|pmc=PMC2705234}}</ref>
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|NGS
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|✓
			\|-
			\|}
			\|}