[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/tblab/nrc/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","tblab","reponame","nrc","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":62,"_64":65,"_66":-5,"_67":68,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2017-01-19T14:42:06.014711Z","description","nRC: non-coding RNA Classifier","is_private","last_updated","2017-01-19T14:42:06.794578Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",1868,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","### nRC: non-coding RNA Classifier\n\n#### This image, based on Centos (7.2.1511) image, contains:\n* Python (2.7.5)\n* Theano (0.8.2)\n* NumPy (1.11.2)\n* Pyyaml (3.12)\n* Java JDK (1.8.0)\n* ViennaRNA (1.8.5)\n* Ipknot (0.0.2)\n* GLPK\t(4.60)\n* MoSS (2.13)\n* NRC-tool (0.0.1)\n\n#### nRC-tool source code:\nhttps://github.com/IcarPA-TBlab/nrc\n\n#### The following command starts a container with the NRC tool.\n```console\ndocker run -d -it --name= -v /data:/root/nrc_workspace/data tblab/nrc\n```\n\n#### . \n#### nRC Training process\n##### Step 1: training feature model\n```console\ndocker exec -it /root/nrc_workspace/nrc_training_feature_model.sh -d .fasta -o -n -m \n```\n##### Step 2: traning CNN (create classification model)\n```console\ndocker exec -it /root/nrc_workspace/nrc_training_network_model.sh -d __.txt -p \n```\n\n#### . \n#### nRC Testing process\n\n##### Step 3: testing feature model\n```console\ndocker exec -it /root/nrc_workspace/nrc_testing_feature_model.sh -d .fasta -f __.nel -o \n```\n##### Step 4: testing CNN (test classification model)\n```console\ndocker exec -it /root/nrc_workspace/nrc_testing_network_model.sh -d -p -m __.pkl -o \n```\n#### .\n\n#### Fasta file format\nNote that each sequence in fasta format should have the following header:\n```console\n>seq_ID class_name\n```\nwher _seq_ID_ and _class_name_ labels must be without \".\",\"\\\",\"/\" or any special character, e.g.:\n```console\n>RF00005_AAFR03000905_1_148681-148750 tRNA\nAGCAGTGTGGCATAGTGGAAAGTGTTGGATTTGTAGTTAAAGGACTTGGGTTCAGATCCC\nTGCTCTGTTA\n```\n#### .\n\n#### Example:\n1) Download example data from this [link](http://tblab.pa.icar.cnr.it/public/nRC/sample_dataset/).\n2) Put example data in a folder on your PC, e.g. /home//nrc/data/.\n3) Open a terminal, then execute the following code.\n\n```console\ndocker run -d -it --name=nrc_tool -v /home//nrc/data:/root/nrc_workspace/data tblab/nrc\n\ndocker exec -it nrc_tool /root/nrc_workspace/nrc_training_feature_model.sh -d sample_train_40.fasta -o experiment1 -n 5 -m 3 \n\ndocker exec -it nrc_tool /root/nrc_workspace/nrc_training_network_model.sh -d experiment1_5_3.txt -p parameters.txt\n\ndocker exec -it nrc_tool /root/nrc_workspace/nrc_testing_feature_model.sh -d sample_test_20.fasta -f experiment1_5_3.nel -o my_test_seqs\n\ndocker exec -it nrc_tool /root/nrc_workspace/nrc_testing_network_model.sh -d my_test_seqs -p parameters.txt -m experiment1_5_3.pkl -o my_first_results.txt\n```\n#### .\n\n#### Additional dataset:\nDataset used for experiments in the manuscript submitted for pubblication at international journal is available [here](http://tblab.pa.icar.cnr.it/public/nRC/paper_dataset/). \nIt is composed by a training dataset with 6320 ncRNA fasta sequences (belonging to 13 ncRNA classes) and two validation datasets with respectively 2600 fasta sequences (13 classes) and 2400 ncRNA fasta sequences (12 classes). All of them are extracted from Rfam database release 12. \nThis link also contains trained models used in the manuscript submitted for pubblication at international journal.","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",576519075,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":65,"_128":21},"content_type","creator",883832,"full_size",576513055,"id",7541526,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":65,"_117":-5},"architecture","amd64","digest","sha256:798ae8b4b9a7fda0965586f085a850cadd078055313225c0af22d7e7d9c1cf92","features","","last_pulled","2026-09-30T06:02:21.129996392Z","last_pushed","2017-01-19T14:42:06Z","os","linux","os_features","os_version","size","variant","2017-01-19T14:42:05.929503Z","last_updater","last_updater_username","media_type","latest","repository",1185901,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":142,"_149":150,"_136":159,"_160":11},{"_40":143,"_42":144,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":145,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":62,"_64":65,"_66":-5,"_67":68,"_69":70,"_71":11,"_72":33,"_73":146,"_79":11,"_80":148,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":147},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_151":62,"_152":-5,"_153":-5,"_154":155},"count","next","previous","results",[156],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":157,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":65,"_128":21},[158],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":65,"_117":-5},[],"canDeleteTags","actionData","errors"]

tblab/nrc

Tags for tblab/nrc