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[ { "id": "workflow1", "annotations": [ { "startX": 110.0, "startY": 44.0, "endX": 6.0, "endY": 5.0, "title": "Alignment", "url": "https://bio.tools/tool/MUSCLE/version/1", "description": "MUSCLE", "edam_term": "multiple sequence alignment", "edam_uri": "http://edamontology.org/operation_0492" }, { "startX": 140.0, "startY": 5.0, "endX": 245.0, "endY": 46.0, "title": "Curation", "url": "https://bio.tools/tool/gblocks/version/0.91b", "description": "Gblocks", "edam_term": "sequence alignment analysis (conservation)", "edam_uri": "http://edamontology.org/operation_0448" }, { "startX": 274.0, "startY": 6.0, "endX": 378.0, "endY": 43.0, "title": "Phylogeny", "url": "https://bio.tools/tool/phyml/version/20130219.patch", "description": "PhyML", "edam_term": "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "edam_uri": "http://edamontology.org/operation_0547" }, { "startX": 408.0, "startY": 4.0, "endX": 512.0, "endY": 44.0, "title": "Tree Rendering", "url": 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"", "edam_uri": "" }, { "startX": 482.0, "startY": 59.0, "endX": 613.0, "endY": 99.0, "title": "Remove PCR adapters", "url": "https://bio.tools/tool/cutadapt/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 485.0, "startY": 129.0, "endX": 619.0, "endY": 168.0, "title": "Remove duplicates", "url": "https://bio.tools/tool/prinseq/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 484.0, "startY": 195.0, "endX": 616.0, "endY": 234.0, "title": "Remove potential contaminants by similarity search", "url": "https://bio.tools/tool/blat/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 378.0, "startY": 0.0, "endX": 510.0, "endY": 40.0, "title": "Raw reads", "url": "http://edamontology.org/data_3497", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 379.0, "startY": 318.0, "endX": 512.0, "endY": 361.0, "title": "Cleaned reads", "url": "http://edamontology.org/data_2977", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 375.0, "startY": 386.0, "endX": 515.0, "endY": 433.0, "title": "De novo assembly of the reads", "url": "https://bio.tools/tool/trinity/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 143.0, "startY": 494.0, "endX": 279.0, "endY": 536.0, "title": "Checking the assembly quality", "url": "", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 145.0, "startY": 563.0, "endX": 275.0, "endY": 604.0, "title": "Functional annotation", "url": "https://bio.tools/tool/HMMER/version/1", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 278.0, "startY": 630.0, "endX": 412.0, "endY": 670.0, "title": "Similarity serch", "url": "https://bio.tools/tool/NCBI_BLAST/version/1", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 281.0, "startY": 717.0, "endX": 410.0, "endY": 757.0, "title": "Functional annotation", "url": "https://bio.tools/tool/blast2go/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 517.0, "startY": 567.0, "endX": 672.0, "endY": 614.0, "title": "Aligning reads to transcripts", "url": "https://bio.tools/tool/bowtie2/version/2.2.8", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 518.0, "startY": 654.0, "endX": 667.0, "endY": 695.0, "title": "Reads aligned to transcripts", "url": "http://edamontology.org/data_1383", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 512.0, "startY": 742.0, "endX": 673.0, "endY": 780.0, "title": "Expression quantification", "url": "https://bio.tools/tool/RSEM/version/none", "description": "", "edam_term": "", "edam_uri": "" }, { "startX": 379.0, "startY": 490.0, "endX": 513.0, "endY": 532.0, "title": "Transcripts", "url": "http://edamontology.org/data_3494", "description": "", "edam_term": "", "edam_uri": "" } ], "width": 758.0, "height": 830.0, "image": "/media/workflows/e200925a-c7d.png", "description": "TRUFA (Transcriptomes User-Friendly Analysis) is a free webserver designed to help you perform RNA-seq analysis.", "sourceURL": "https://trufa.ifca.es/web/" }, { "id": "workflow3", "annotations": [ { "startX": 8.0, "startY": 26.0, "endX": 70.0, "endY": 53.0, "title": "fasta", "url": "http://edamontology.org/format_1929", "description": "FASTA file format", "edam_term": "FASTA", "edam_uri": "http://edamontology.org/format_1929" }, { "startX": 72.0, "startY": 27.0, "endX": 130.0, "endY": 55.0, "title": "fastq", "url": "http://edamontology.org/format_1930", "description": "FASTQ file format", "edam_term": "FASTQ", "edam_uri": "http://edamontology.org/format_1930" }, { "startX": 131.0, "startY": 28.0, "endX": 186.0, "endY": 54.0, "title": "bam", "url": "http://edamontology.org/format_2572", "description": "BAM file format", "edam_term": "BAM", "edam_uri": "http://edamontology.org/format_2572" }, { "startX": 266.0, "startY": 97.0, "endX": 467.0, "endY": 170.0, "title": "qQCReport()", "url": 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It is used to count alignments in known genomic intervals (promoters, exons, genes, etc.) or in peak regions identified outside of QuasR.", "edam_term": "", "edam_uri": "" }, { "startX": 330.0, "startY": 402.0, "endX": 104.0, "endY": 329.0, "title": "qProfile()", "url": "", "description": "qProfile is similar to qCount, with the main difference that it returns a spatial profile of counts with the number of alignments at different positions relative to the query.", "edam_term": "", "edam_uri": "" }, { "startX": 107.0, "startY": 440.0, "endX": 362.0, "endY": 507.0, "title": "qMeth()", "url": "", "description": "qMeth is used in Bis-seq experiments to obtain the numbers of methylated and unmethylated cytosines for selected sequence contexts.", "edam_term": "", "edam_uri": "" }, { "startX": -1.0, "startY": 96.0, "endX": 211.0, "endY": 196.0, "title": "qProject", "url": "", "description": "The user interface of QuasR consists of only a handful of functions (Fig. 1) and a single class (qProject) that is returned by qAlign and serves as input to all downstream processing.", "edam_term": "", "edam_uri": "" }, { "startX": 267.0, "startY": 0.0, "endX": 544.0, "endY": 62.0, "title": "qAlign()", "url": "", "description": "By default, qAlign uses bowtie to align single or paired-end reads to a reference genome, and unmapped reads are optionally further aligned to alternative references, for example to quantify the level of vector contamination.", "edam_term": "", "edam_uri": "" } ], "width": 706.0, "height": 524.0, "image": "/media/workflows/77b7f27d-0e9.jpg", "description": "QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read\npreprocessing, alignment and quality control to quantification.", "sourceURL": "https://www.ncbi.nlm.nih.gov/pubmed/25417205" }, { "id": "workflow4", "annotations": [ { "startX": 175.0, "startY": 95.0, "endX": 461.0, "endY": 151.0, "title": "Paired-end sequencing reads", "url": "", "description": "Fluorescence trace data generated by an automated DNA sequencer", "edam_term": "Sequence trace", "edam_uri": "http://edamontology.org/data_0924" }, { "startX": 181.0, "startY": 198.0, "endX": 298.0, "endY": 255.0, "title": "Read Alignment", "url": "", "description": "Read pairs are first independently aligned", "edam_term": "DNA mapping", "edam_uri": "http://edamontology.org/operation_2520" }, { "startX": 348.0, "startY": 197.0, "endX": 467.0, "endY": 254.0, "title": "Read Alignment", "url": "", "description": "Read pairs are first independently aligned", "edam_term": "DNA mapping", "edam_uri": "http://edamontology.org/operation_2520" }, { "startX": 44.0, "startY": 246.0, "endX": 170.0, "endY": 390.0, "title": "Filtering", "url": "", "description": "Low mapping quality reads, multiple hits and singletons can be discarded", "edam_term": "Filtering", "edam_uri": "http://edamontology.org/operation_3695" }, { "startX": 212.0, "startY": 306.0, "endX": 428.0, "endY": 341.0, "title": "Read Pairing", "url": "", "description": "Both mapping steps are merged in a single alignment file", "edam_term": "Sequence merging", "edam_uri": "http://edamontology.org/operation_0232" }, { "startX": 179.0, "startY": 380.0, "endX": 454.0, "endY": 413.0, "title": "Assignment to Parental Genome", "url": "", "description": "If phased genotyping data and N-masked genome are provided, it will align assign them to a parental genome", "edam_term": "Sequence annotation", "edam_uri": "http://edamontology.org/operation_0361" }, { "startX": 158.0, "startY": 450.0, "endX": 481.0, "endY": 483.0, "title": "Assignment to Restriction Fragment", "url": "", "description": "Read pairs are assigned to a restriction fragment and invalid ligation products will be filtered out", "edam_term": "Sequence annotation, Filtering", "edam_uri": "http://edamontology.org/operation_0361\n" }, { "startX": 180.0, "startY": 609.0, "endX": 460.0, "endY": 643.0, "title": "Combine Multiple Samples", "url": "", "description": "", "edam_term": "Sequence merging", "edam_uri": "http://edamontology.org/operation_0232" }, { "startX": 182.0, "startY": 678.0, "endX": 458.0, "endY": 712.0, "title": "Select Allele-specific Pairs", "url": "", "description": "Only pairs with at least one allele-specific reads are used to build contact maps", "edam_term": "Filtering", "edam_uri": "http://edamontology.org/operation_3695" }, { "startX": 213.0, "startY": 746.0, "endX": 426.0, "endY": 778.0, "title": "Raw Contact Maps", "url": "", "description": "Genome is divided into bins of equal size, and the number of contacts observed between each pair of bins is reported", "edam_term": "Matrix, Matrix Format", "edam_uri": "http://edamontology.org/data_2082" }, { "startX": 197.0, "startY": 813.0, "endX": 441.0, "endY": 841.0, "title": "Normalized Contact Maps", "url": "", "description": "Normalization is applied to remove Hi-C systematic bias on the genome-wide contact map", "edam_term": "Matrix, Matrix Format", "edam_uri": "http://edamontology.org/data_2082" } ], "width": 677.0, "height": 859.0, "image": "/media/workflows/d29a46d6-27c.png", "description": "HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.", "sourceURL": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x" }, { "id": "workflow5", "annotations": [ { "startX": 156.0, "startY": 1.0, "endX": 459.0, "endY": 250.0, "title": "Image acquisition", "url": "", "description": "Biological laboratories usually acquire images by measuring photon flux. Although capturing an image from a camera into the computer is straightforward, in mostcases image acquisition needs to be tightly synchronized with other computer-controllable equipment such as shutters, filter wheels, XY stages, Z-axis focus drives, and autofocus mechanisms. This automation is necessary in orderto gather the appropriate information from a sample or to allow the unattended acquisition of large numbers of images in time-lapse series, z-stacks, multiple spatial locations in a largesample, or multiple samples in a large-scale experiment.", "edam_term": "Imaging, Data acquisition", "edam_uri": "http://edamontology.org/topic_3382" }, { "startX": 58.0, "startY": 270.0, "endX": 563.0, "endY": 576.0, "title": "Image storage", "url": "", "description": "Image databases provide integrated platforms to organize, search, process, analyze, share and visualize data associated with biological experiments—including both images and metadata.", "edam_term": "Data management", "edam_uri": "http://edamontology.org/topic_3071" }, { "startX": 654.0, "startY": 497.0, "endX": 812.0, "endY": 573.0, "title": "Image annotation", "url": "", "description": "Image annotation is the process of associating images with metadata (i.e., information about the images, including information about how the images and the samples therein were created, as well as information about the content of the image itself).", "edam_term": "Data submission, annotation and curation", "edam_uri": "http://edamontology.org/topic_0219" }, { "startX": 655.0, "startY": 281.0, "endX": 811.0, "endY": 352.0, "title": "Deposition to public image repositories", "url": "", "description": "Some public bioimage data repositories are geared towards education and outreach, others gather sets of images that accompany published papers, others are more focused on providing research resources.", "edam_term": "Deposition", "edam_uri": "http://edamontology.org/operation_3431" }, { "startX": 655.0, "startY": 397.0, "endX": 811.0, "endY": 445.0, "title": "Ontologies", "url": "", "description": "Ontologies are formal expressions of human knowledge about a domain in machine readable form. Ontologies enable the consistent description of image metadata. They can also enable consistent description of visual annotations by defining a set of classes and the relationships between them.", "edam_term": "Ontology", "edam_uri": "http://edamontology.org/data_0582" }, { "startX": 655.0, "startY": 713.0, "endX": 811.0, "endY": 783.0, "title": "Machine learning", "url": "", "description": "Machine learning in bioimaging is mainly used for classification – classification of either individual pixels, regions of interest in images, or whole images.", "edam_term": "Machine learning", "edam_uri": "http://edamontology.org/topic_3474" }, { "startX": 655.0, "startY": 801.0, "endX": 812.0, "endY": 896.0, "title": "Bioimaging libraries and toolkits", "url": "", "description": "A library is a collection of low-level algorithms that can be used, by those with programming experience, either directly or as pieces upon which end-user software applications can be built.", "edam_term": "EDAM-bioimaging", "edam_uri": "http://webprotege.stanford.edu/R9TrjymduaijOFxNNs4OmtV" }, { "startX": 156.0, "startY": 595.0, "endX": 459.0, "endY": 923.0, "title": "Image analysis and visualisation", "url": "", "description": "", "edam_term": "Image analysis, Microscope image visualisation", "edam_uri": "http://edamontology.org/operation_3443" } ], "width": 850.0, "height": 925.0, "image": "/media/workflows/d4f56b5d-370.png", "description": "Computational steps that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options. ", "sourceURL": "https://www.researchgate.net/figure/228087863_fig7_Figure-1-Overview-of-imaging-workflowModern-bioimaging-requires-the-use-of-software" }, { "id": "workflow6", "annotations": [ { "startX": 156.0, "startY": 1.0, "endX": 459.0, "endY": 250.0, "title": "Image acquisition", "url": "", "description": "Biological laboratories usually acquire images by measuring photon flux. Although capturing an image from a camera into the computer is straightforward, in mostcases image acquisition needs to be tightly synchronized with other computer-controllable equipment such as shutters, filter wheels, XY stages, Z-axis focus drives, and autofocus mechanisms. This automation is necessary in orderto gather the appropriate information from a sample or to allow the unattended acquisition of large numbers of images in time-lapse series, z-stacks, multiple spatial locations in a largesample, or multiple samples in a large-scale experiment.", "edam_term": "Imaging, Data acquisition", "edam_uri": "http://edamontology.org/topic_3382" }, { "startX": 58.0, "startY": 270.0, "endX": 563.0, "endY": 576.0, "title": "Image storage", "url": "", "description": "Image databases provide integrated platforms to organize, search, process, analyze, share and visualize data associated with biological experiments—including both images and metadata.", "edam_term": "Data management", "edam_uri": "http://edamontology.org/topic_3071" }, { "startX": 654.0, "startY": 497.0, "endX": 812.0, "endY": 573.0, "title": "Image annotation", "url": "", "description": "Image annotation is the process of associating images with metadata (i.e., information about the images, including information about how the images and the samples therein were created, as well as information about the content of the image itself).", "edam_term": "Data submission, annotation and curation", "edam_uri": "http://edamontology.org/topic_0219" }, { "startX": 655.0, "startY": 281.0, "endX": 811.0, "endY": 352.0, "title": "Deposition to public image repositories", "url": "", "description": "Some public bioimage data repositories are geared towards education and outreach, others gather sets of images that accompany published papers, others are more focused on providing research resources.", "edam_term": "Deposition", "edam_uri": "http://edamontology.org/operation_3431" }, { "startX": 655.0, "startY": 397.0, "endX": 811.0, "endY": 445.0, "title": "Ontologies", "url": "", "description": "Ontologies are formal expressions of human knowledge about a domain in machine readable form. 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