{"id":88,"date":"2022-10-18T15:44:50","date_gmt":"2022-10-18T15:44:50","guid":{"rendered":"http:\/\/schellackia.sickkids.ca\/wordpress\/?page_id=88"},"modified":"2023-09-27T15:56:52","modified_gmt":"2023-09-27T15:56:52","slug":"tools-2","status":"publish","type":"page","link":"https:\/\/compsysbio.org\/index.php\/tools-2\/","title":{"rendered":".\/tools"},"content":{"rendered":"\n<div class=\"wp-block-group alignwide is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\">\n<div class=\"wp-block-group alignwide is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\"><\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:26% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"1856\" height=\"1856\" src=\"https:\/\/compsysbio.org\/wp-content\/uploads\/2022\/10\/tools.png\" alt=\"\" class=\"wp-image-50 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\">\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<ul class=\"has-large-font-size wp-block-list\">\n<li><a href=\"#bacteriome\" data-type=\"page\">Bacteriome<\/a><\/li>\n\n\n\n<li><a href=\"#cellpp\">Cell<\/a>4D<\/li>\n\n\n\n<li><a href=\"#subseqer\">SubSeqer<\/a><\/li>\n\n\n\n<li><a href=\"#phylopro\">PhyloPro<\/a><\/li>\n<\/ul>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<ul class=\"has-large-font-size wp-block-list\">\n<li><a href=\"#metapro\">MetaPro<\/a><\/li>\n\n\n\n<li><a href=\"#hyperscape\">HyperScape<\/a><\/li>\n\n\n\n<li><a href=\"#popnetd3\">PopNetD3<\/a><\/li>\n\n\n\n<li><a href=\"#architect\" data-type=\"internal\" data-id=\"#architect\">Architect<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"bacteriome\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-2 \" id=\"oxi-image-hover-wrapper-2\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"http:\/\/bacteriome.org\/\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/B2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">Bacteriome<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledge base.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"cellpp\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-3 \" id=\"oxi-image-hover-wrapper-3\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/sourceforge.net\/projects\/cellpp\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/C2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">Cell++<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>Cell4D is a novel stochastic simulation environment that is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways, and intracellular calcium signaling.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"hyperscape\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-4 \" id=\"oxi-image-hover-wrapper-4\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/www.compsysbio.org\/subseqer\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/S2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">SubSeqr<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>SubSeqer is a webtool aimed at uncovering meaningful sequence motifs in low complexity protein sequences. It uses a novel subsequence visualization method to build motifs by identifying relationships between small subsequences within the larger sequence.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"phylopro\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-5 \" id=\"oxi-image-hover-wrapper-5\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/www.compsysbio.org\/phylopro\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/P2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">PhyloPro<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"metapro\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-6 \" id=\"oxi-image-hover-wrapper-6\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/github.com\/ParkinsonLab\/MetaPro\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/M2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">MetaPro<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>The MetaPro Meta Transcriptomics\/Genomics Pipeline is a software tool that will perform Transcriptomics and Genomic analysis on Paired and Single Reads of FASTQ data.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"subseqer\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-7 \" id=\"oxi-image-hover-wrapper-7\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/www.compsysbio.org\/hyperscape\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/H2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">HyperScape<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>HyperScape is a novel hypergraph implementation that better captures hierarchical structures, using components of elastic fibers and chromatin modification as models.<\/p>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"popnetd3\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-9 \" id=\"oxi-image-hover-wrapper-9\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/www.compsysbio.org\/popnetd3\/\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/Pn2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">PopNetD3<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>PopNet is an analysis and visualization tool for population genetics. PopNetD3 allows for the simple, streamlined analysis of your population of interest without the hassle of Linux, programming, or external packages.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"background-color:#212121;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"architect\">            <div class=\"oxi-addons-container noLightbox oxi-image-hover-wrapper-8 \" id=\"oxi-image-hover-wrapper-8\">\n                <div class=\"oxi-addons-row\">\n                                <div class=\"oxi-image-hover-style oxi-bt-col-lg-12 oxi-bt-col-md-12 oxi-bt-col-sm-12                         \" >\n                <div class=\"oxi-image-hover-style-caption\">\n                    <div class=\"oxi-image-hover oxi-image-caption-hover oxi-image-caption-hover-style-9 oxi-image-fade-in-down\">\n                                                    <a  href=\"https:\/\/github.com\/ParkinsonLab\/Architect\" target=\"_blank\">\n                                                                                    <div class=\"oxi-image-hover-figure\">\n                                <div class=\"oxi-image-hover-image\">\n                                    <img decoding=\"async\" src=\"http:\/\/compsysbio.org\/wp-content\/uploads\/2022\/11\/A2.png\" >\n                                <\/div>\n                                <div class=\"oxi-image-hover-figure-caption\">\n                                    <div class=\"oxi-image-hover-caption-tab image-hover-align-center-center\">\n                                                                                    <h3 class=\"oxi-image-hover-heading iheu-fade-up \">Architect<\/h3>\n                                                                                    <\/div>\n                                <\/div>\n                            <\/div>\n                                                        <\/a>\n\t\t\t\t\t\t\t\t                    <\/div>\n                <\/div>\n                            <\/div>\n                            <\/div>\n            <\/div>\n\t\t\t\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\"\/>\n\n\n\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\">\n<p>Pipeline for automatic metabolic model reconstruction using an ensemble method for enzyme annotation.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column has-foreground-background-color has-background is-layout-flow wp-block-column-is-layout-flow\" style=\"padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px\" id=\"subseqer\">\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\" style=\"padding-top:15px;padding-right:15px;padding-bottom:15px;padding-left:15px\"><\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledge base. Cell4D is a novel stochastic simulation environment that is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways, and intracellular calcium signaling. SubSeqer is a webtool aimed at uncovering meaningful sequence motifs in [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-88","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/88","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/comments?post=88"}],"version-history":[{"count":42,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/88\/revisions"}],"predecessor-version":[{"id":449,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/88\/revisions\/449"}],"wp:attachment":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/media?parent=88"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}