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ElDeveloper/embedded_figure_1.ipynb

Created December 11, 2017 23:23
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embedded_figure_1.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Embedded Figure 1 from \"Deblur rapidly resolves single-nucleotide community sequence patterns\" showing merged _de novo_ OTU picking runs. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pandas as pd\n",
"import skbio\n",
"from emperor import Emperor, nbinstall\n",
"nbinstall()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<script type=\"text/javascript\">\n",
"\n",
"if ($(\"#emperor-css\").length == 0){{\n",
" $(\"head\").append([\n",
"\n",
" '<link id=\"emperor-css\" rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/css/emperor.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/jquery-ui.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/slick.grid.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/spectrum.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/chosen.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/jquery.contextMenu.min.css\">'\n",
" ]);\n",
"}}\n",
"</script>\n",
"\n",
"<div id='emperor-notebook-0x2149b97f' style=\"position: relative; width:100%; height:500px;\">\n",
" <div class='loading' style=\"position: absolute;top: 50%;left: 50%;margin-left: -229px; margin-top: -59px; z-index: 10000;height:118px;width:458px;padding:0px\"><img src='https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/img/emperor.png' alt='Emperor resources missing. Expected them to be found in https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files'></div>\n",
"</div>\n",
"</div>\n",
"\n",
"<script type=\"text/javascript\">\n",
"requirejs.config({\n",
"// the left side is the module name, and the right side is the path\n",
"// relative to the baseUrl attribute, do NOT include the .js extension\n",
"'paths': {\n",
" /* jQuery */\n",
" 'jquery': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery-2.1.4.min',\n",
" 'jqueryui': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery-ui.min',\n",
" 'jquery_drag': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.event.drag-2.2.min',\n",
"\n",
" /* jQuery plugins */\n",
" 'chosen': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/chosen.jquery.min',\n",
" 'spectrum': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/spectrum.min',\n",
" 'position': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.ui.position.min',\n",
" 'contextmenu': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.contextMenu.min',\n",
"\n",
" /* other libraries */\n",
" 'underscore': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/underscore-min',\n",
" 'chroma': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/chroma.min',\n",
" 'filesaver': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/FileSaver.min',\n",
" 'blob': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/Blob',\n",
" 'canvastoblob': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/canvas-toBlob',\n",
" 'd3': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/d3.min',\n",
"\n",
" /* THREE.js and plugins */\n",
" 'three': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.min',\n",
" 'orbitcontrols': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/OrbitControls',\n",
" 'projector': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/Projector',\n",
" 'svgrenderer': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/SVGRenderer',\n",
" 'canvasrenderer': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/CanvasRenderer',\n",
"\n",
" /* SlickGrid */\n",
" 'slickcore': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.core.min',\n",
" 'slickgrid': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.grid.min',\n",
" 'slickformatters': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.editors.min',\n",
" 'slickeditors': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.formatters.min',\n",
"\n",
" /* Emperor's objects */\n",
" 'util': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/util',\n",
" 'model': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/model',\n",
" 'view': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/view',\n",
" 'controller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/controller',\n",
" 'draw': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/draw',\n",
" 'scene3d': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/sceneplotview3d',\n",
" 'abcviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/abc-view-controller',\n",
" 'viewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/view-controller',\n",
" 'colorviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/color-view-controller',\n",
" 'visibilitycontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/visibility-controller',\n",
" 'scaleviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/scale-view-controller',\n",
" 'shapecontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/shape-controller',\n",
" 'axescontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/axes-controller',\n",
" 'shape-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/shape-editor',\n",
" 'color-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/color-editor',\n",
" 'scale-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/scale-editor',\n",
" 'shapes': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/shapes'\n",
"},\n",
"/*\n",
" Libraries that are not AMD compatible need shim to declare their\n",
" dependencies.\n",
" */\n",
"'shim': {\n",
" 'jquery_drag': {\n",
" 'deps': ['jquery', 'jqueryui']\n",
" },\n",
" 'chosen': {\n",
" 'deps': ['jquery'],\n",
" 'exports': 'jQuery.fn.chosen'\n",
" },\n",
" 'contextmenu' : {\n",
" 'deps': ['jquery', 'jqueryui', 'position']\n",
" },\n",
" 'filesaver' : {\n",
" 'deps': ['blob']\n",
" },\n",
" 'canvastoblob' : {\n",
" 'deps': ['blob']\n",
" },\n",
" 'orbitcontrols': {\n",
" 'deps': ['three']\n",
" },\n",
" 'projector': {\n",
" 'deps': ['three']\n",
" },\n",
" 'svgrenderer': {\n",
" 'deps': ['orbitcontrols', 'projector']\n",
" },\n",
" 'canvasrenderer': {\n",
" 'deps': ['orbitcontrols', 'projector']\n",
" },\n",
"'slickcore': ['jqueryui'],\n",
"'slickgrid': ['slickcore', 'jquery_drag', 'slickformatters',\n",
" 'slickeditors']\n",
"}\n",
"});\n",
"\n",
"requirejs(\n",
"[\"jquery\", \"model\", \"controller\"],\n",
"function($, model, EmperorController) {\n",
" var DecompositionModel = model.DecompositionModel;\n",
"\n",
" var div = $('#emperor-notebook-0x2149b97f');\n",
"\n",
" var data = {\n",
" // coordinates information\n",
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" 'axes_names': [0, 1, 2, 3, 4],\n",
" 'percents_explained': [3.9310348878299997, 3.9079440139300003, 3.19599122527, 2.7754763199299997, 2.37033248935],\n",
"\n",
" // sample information\n",
" 'metadata_headers': [\"SampleID\", \"VIOSCREEN_MANNITOL\", \"VIOSCREEN_SFA100\", \"NON_FOOD_ALLERGIES_BEESTINGS\", \"VIOSCREEN_FINISHED\", \"TONSILS_REMOVED\", \"VIOSCREEN_SFA170\", \"VIOSCREEN_VEGETABLE_SERVINGS\", \"VIOSCREEN_SORBITOL\", \"COUNTRY_OF_BIRTH\", \"PETS_OTHER\", \"ECONOMIC_REGION\", \"VIOSCREEN_SFA80\", \"VIOSCREEN_BETACAR\", \"CANCER_TREATMENT\", \"VIOSCREEN_LOW_FAT_DAIRY_SERVING\", \"VIOSCREEN_NIACINEQ\", \"LinkerPrimerSequence\", \"VIOSCREEN_GAMMTOCO\", \"VIOSCREEN_LYSINE\", \"VIOSCREEN_ISOMALT\", \"LIVER_DISEASE\", \"BODY_PRODUCT\", \"VIOSCREEN_DATABASE\", \"ARTIFICIAL_SWEETENERS\", \"VIOSCREEN_SUCROSE\", \"ENA-BASE-COUNT\", \"VIOSCREEN_CLAC9T11\", \"SUBSET_HEALTHY\", \"VIOSCREEN_FIBER\", \"VIOSCREEN_LACTITOL\", \"VIOSCREEN_HEI_NON_JUICE_FRT\", \"CONTRACEPTIVE\", \"ALLERGIC_TO_UNSPECIFIED\", \"VIOSCREEN_OXALICM\", \"VIOSCREEN_ALPHACAR\", \"SALTED_SNACKS_FREQUENCY\", \"ALCOHOL_TYPES_UNSPECIFIED\", \"AGE_CAT\", \"VIOSCREEN_LYCOPENE\", \"VIOSCREEN_VEG5_DAY\", 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\"VIOSCREEN_WHOLE_GRAIN_SERVINGS\", \"VIOSCREEN_HEI2010_PROTIEN_FOODS\", \"ENV_FEATURE\", \"NAIL_BITER\", \"VIOSCREEN_NCCGLGR\", \"VIOSCREEN_OXALIC\", \"VIOSCREEN_HEI_FRUIT\", \"VIOSCREEN_QUESTIONNAIRE\", \"VITAMIN_D_SUPPLEMENT_FREQUENCY\", \"ADD_ADHD\", \"READY_TO_EAT_MEALS_FREQUENCY\", \"VIOSCREEN_MFA161\", \"VIOSCREEN_SATOCO\", \"VIOSCREEN_RIBOFLA\", \"VIOSCREEN_STARCH\", \"VIOSCREEN_MFA221\", \"IBD\", \"CAT\", \"HOST_TAXID\", \"VIOSCREEN_V_TOTAL\", \"VIOSCREEN_V_ORANGE\", \"IBS\", \"VIOSCREEN_M_FRANK\", \"COLLECTION_TIMESTAMP\", \"VIOSCREEN_DELTTOCO\", \"MULTIVITAMIN\", \"CANCER\", \"ACNE_MEDICATION_OTC\", \"VIOSCREEN_FRUIT_SERVINGS\", \"ALLERGIC_TO_I_HAVE_NO_FOOD_ALLERGIES_THAT_I_KNOW_OF\", \"DIABETES\", \"CDIFF\", \"MENTAL_ILLNESS_TYPE_BIPOLAR_DISORDER\", \"ALLERGIC_TO_OTHER\", \"VIOSCREEN_BETATOCO\", \"HEIGHT_CM\", \"VIOSCREEN_FRIED_FOOD_SERVINGS\", \"VIOSCREEN_FISH_SERVINGS\", \"CHICKENPOX\", \"VIOSCREEN_FRTSUMM\", \"VIOSCREEN_GRAMS\", \"ASSIGNED_FROM_GEO\", \"VIOSCREEN_VALINE\", \"VIOSCREEN_HEI_SODIUM\", \"BODY_SITE\", \"VIOSCREEN_HISTIDIN\", \"VIOSCREEN_BETAINE\", \"VIOSCREEN_ALCOHOL_SERVINGS\", \"FUNGAL_OVERGROWTH\", \"FLOSSING_FREQUENCY\", \"ONE_LITER_OF_WATER_A_DAY_FREQUENCY\", \"COSMETICS_FREQUENCY\", \"HOST_SUBJECT_ID\", \"VIOSCREEN_SFATOT\", \"VIOSCREEN_POTASS\", \"VIOSCREEN_PHYTIC\", \"NON_FOOD_ALLERGIES_SUN\", \"VIOSCREEN_PECTINS\", \"CARDIOVASCULAR_DISEASE\", \"VIOSCREEN_SFA180\", \"VIOSCREEN_FOL_SYN\", \"VIOSCREEN_F_NJ_TOTAL\", \"VIOSCREEN_A_CAL\", \"FED_AS_INFANT\", \"VIOSCREEN_V_TOMATO\", \"VIOSCREEN_LEUCINE\", \"WEIGHT_UNITS\", \"VIOSCREEN_ACTIVITY_LEVEL\", \"VIOSCREEN_CALORIES\", \"COUNTRY\", \"ACID_REFLUX\", \"VIOSCREEN_GENDER\", \"COMMON_NAME\", \"VIOSCREEN_A_BEV\", \"VIOSCREEN_HEI2010_EMPTY_CALORIES\", \"NON_FOOD_ALLERGIES_UNSPECIFIED\", \"FLU_VACCINE_DATE\", \"PREGNANT\", \"BMI\", \"CENSUS_REGION\", \"TEETHBRUSHING_FREQUENCY\", \"LAST_MOVE\", \"DEPRESSION_BIPOLAR_SCHIZOPHRENIA\", \"FROZEN_DESSERT_FREQUENCY\", \"LIVINGWITH\", \"CLINICAL_CONDITION\", \"VIOSCREEN_SCFV\", \"VIOSCREEN_LEGUMES\", \"VIOSCREEN_BETACRYP\", \"VIOSCREEN_HEI2010_SODIUM\", \"VIOSCREEN_PROTOCOL\", \"ALTITUDE\", \"LAST_TRAVEL\", \"DNA_EXTRACTED\", \"VIOSCREEN_TRYPTOPH\", \"VIOSCREEN_TOTALTFA\", \"ROOMMATES\", \"VIOSCREEN_ALCOHOL\", \"VIOSCREEN_SACCHAR\", \"VIOSCREEN_ERYTHR\", \"VIOSCREEN_D_TOTAL\", \"VIOSCREEN_F_TOTAL\", \"SEX\", \"ALLERGIC_TO_TREE_NUTS\", \"VIOSCREEN_NON_FRIED_FISH_SERVINGS\", \"ASD\", \"VIVID_DREAMS\", \"LUNG_DISEASE\", \"VIOSCREEN_ADD_SUG\", \"VIOSCREEN_PFA225\", \"VIOSCREEN_PFA226\", \"VIOSCREEN_HEI_SCORE\", \"ALCOHOL_FREQUENCY\", \"POULTRY_FREQUENCY\", \"DOMINANT_HAND\", \"VIOSCREEN_FAT\", \"VIOSCREEN_PROLINE\", \"VIOSCREEN_M_MEAT\", \"ROOMMATES_IN_STUDY\", \"VIOSCREEN_CALCIUM_AVG\", \"VIOSCREEN_WEIGHT\", \"SURVEY_ID\", \"VIOSCREEN_G_WHL\", \"SUBSET_ANTIBIOTIC_HISTORY\", \"VIOSCREEN_PROTANIM\", \"SMOKING_FREQUENCY\", \"MENTAL_ILLNESS\", \"VIOSCREEN_MALTITOL\", \"VIOSCREEN_CALCIUM_SERVINGS\", \"DEPTH\", \"VIOSCREEN_BMI\", \"REQUIRED_SAMPLE_INFO_STATUS\", \"BREASTMILK_FORMULA_ENSURE\", \"VIOSCREEN_FOL_NAT\", \"BarcodeSequence\", \"RACE\", \"MENTAL_ILLNESS_TYPE_DEPRESSION\", \"VIOSCREEN_MAGNES\", \"KIDNEY_DISEASE\", \"VIOSCREEN_VITA_RE\", \"COLLECTION_TIME\", \"VIOSCREEN_VEGSUMM\", \"VIOSCREEN_SFA60\", \"COLLECTION_MONTH\", \"VITAMIN_B_SUPPLEMENT_FREQUENCY\", \"VIOSCREEN_HEI2010_WHOLE_FRUIT\", \"SUBSET_IBD\", \"VIOSCREEN_HEI_SAT_FAT\", \"VIOSCREEN_TOTFOLAT\", \"VIOSCREEN_ARGININE\", \"VIOSCREEN_HEI2010_FATTY_ACIDS\", \"ALCOHOL_TYPES_SOUR_BEERS\", \"VIOSCREEN_PHENYLAL\", \"VIOSCREEN_ALPHTOCE\", \"PHYSICAL_SPECIMEN_LOCATION\", \"VIOSCREEN_PROTEIN\", \"VIOSCREEN_ALPHTOCO\", \"VIOSCREEN_GLTC\", \"VIOSCREEN_MULTI_CALCIUM_DOSE\", \"VIOSCREEN_VITA_IU\", \"MENTAL_ILLNESS_TYPE_PTSD_POSTTRAUMATIC_STRESS_DISORDER\", \"VIOSCREEN_NIACIN\", \"VIOSCREEN_CALCIUM_FREQ\", \"ALCOHOL_TYPES_RED_WINE\", \"ENA-CHECKLIST\", \"GLUTEN\", \"VIOSCREEN_SELENIUM\", \"VIOSCREEN_TOTCLA\", \"VIOSCREEN_EMAIL\", \"WEIGHT_KG\", \"SUBSET_AGE\", \"VIOSCREEN_PFA184\", \"VIOSCREEN_PFA183\", \"VIOSCREEN_PFA182\", \"VIOSCREEN_D_TOT_SOYM\", \"VIOSCREEN_DISCFAT_OIL\", \"VIOSCREEN_GALACTOS\", \"MILK_SUBSTITUTE_FREQUENCY\", \"VIOSCREEN_JUICE_SERVINGS\", \"VIOSCREEN_FRT5_DAY\", \"VIOSCREEN_HEIGHT\", \"VIOSCREEN_PINITOL\", \"VIOSCREEN_CALCIUM\", \"LOWGRAIN_DIET_TYPE\", \"VIOSCREEN_GENISTN\", \"SEAFOOD_FREQUENCY\", \"VIOSCREEN_SFA120\", \"VIOSCREEN_HEI_GRAINS\", \"ALLERGIC_TO_PEANUTS\", \"PROBIOTIC_FREQUENCY\", \"MENTAL_ILLNESS_TYPE_BULIMIA_NERVOSA\", \"VIOSCREEN_METHION\", \"VIOSCREEN_HEI_VEG\", \"VIOSCREEN_GLUCOSE\", \"OLIVE_OIL\", \"VIOSCREEN_EER\", \"VIOSCREEN_CHOLINE\", \"VIOSCREEN_ISOLEUC\", \"VIOSCREEN_FOL_DEQV\", \"VIOSCREEN_COUMEST\", \"VIOSCREEN_TFA161T\", \"SKIN_CONDITION\", \"VIOSCREEN_STARTED\", \"VIOSCREEN_XYLITOL\", \"VIOSCREEN_BIOCHANA\", \"VIOSCREEN_F_NJ_CITMLB\", \"VIOSCREEN_HEI2010_VEG\", \"VIOSCREEN_M_NUTSD\", \"MENTAL_ILLNESS_TYPE_SCHIZOPHRENIA\", \"VIOSCREEN_PFATOT\", \"VIOSCREEN_FIBINSO\", \"TITLE\", \"VIOSCREEN_V_OTHER\", \"VIOSCREEN_WGRAIN\", \"VIOSCREEN_TFA182T\", \"VIOSCREEN_G_TOTAL\", \"ENA-SPOT-COUNT\", \"EXERCISE_LOCATION\", \"VIOSCREEN_M_FISH_LO\", \"NON_FOOD_ALLERGIES_POISON_IVYOAK\", \"VIOSCREEN_VITD2\", \"OTHER_SUPPLEMENT_FREQUENCY\", \"VIOSCREEN_RETINOL\", \"SUBSET_DIABETES\", \"ALLERGIC_TO_SHELLFISH\", \"VIOSCREEN_MFATOT\", \"VIOSCREEN_CYSTINE\", \"FRUIT_FREQUENCY\", \"VIOSCREEN_V_POTATO\", \"VIOSCREEN_PANTOTHE\", \"VIOSCREEN_RECNO\", \"VIOSCREEN_SUBJECT_ID\", \"VIOSCREEN_ASH\", \"HAS_PHYSICAL_SPECIMEN\", \"VIOSCREEN_PHOSPHOR\", \"VIOSCREEN_CALCIUM_FROM_DAIRY_SERVINGS\", \"WHOLE_GRAIN_FREQUENCY\", \"VIOSCREEN_ASPARTIC\", \"VIOSCREEN_V_STARCY\", \"NON_FOOD_ALLERGIES_PET_DANDER\", \"VIOSCREEN_SFA220\", \"COUNTRY_RESIDENCE\", \"SLEEP_DURATION\", \"PUBLIC\", \"VIOSCREEN_F_CITMLB\", \"VIOSCREEN_HEI_WHL_GRAINS\", \"LACTOSE\", \"COLLECTION_SEASON\", \"VIOSCREEN_THREONIN\", \"WHOLE_EGGS\", \"BOWEL_MOVEMENT_QUALITY\", \"VIOSCREEN_BCODEID\", \"MENTAL_ILLNESS_TYPE_SUBSTANCE_ABUSE\", \"TYPES_OF_PLANTS\", \"VIOSCREEN_M_EGG\", \"VIOSCREEN_HEI2010_FRUIT\", \"DEODORANT_USE\", \"VIOSCREEN_DISCFAT_SOL\", \"VIOSCREEN_TYROSINE\", \"VIOSCREEN_WATER\", \"VIOSCREEN_MFA141\", \"VIOSCREEN_HEI2010_SCORE\", \"VIOSCREEN_VITD\", \"LONGITUDE\", \"VIOSCREEN_VITC\", \"WEIGHT_CHANGE\", \"VIOSCREEN_VITK\", \"VIOSCREEN_SFA160\", \"VIOSCREEN_FRUCTOSE\", \"SEASONAL_ALLERGIES\", \"THYROID\", \"VIOSCREEN_ADDSUGAR\", \"VIOSCREEN_MFA201\", \"VIOSCREEN_RGRAIN\", \"VIOSCREEN_V_DRKGR\", \"VIOSCREEN_CALCIUM_DOSE\", \"VIOSCREEN_F_OTHER\", \"ELEVATION\", \"VIOSCREEN_ADSUGTOT\", \"VIOSCREEN_IRON\", \"CSECTION\", \"LEVEL_OF_EDUCATION\", \"VIOSCREEN_ZINC\", \"VIOSCREEN_AVCARB\", \"VIOSCREEN_OMEGA3\", \"VIOSCREEN_TOTSUGAR\", \"VIOSCREEN_NUTRIENT_RECOMMENDATION\", \"ALCOHOL_TYPES_WHITE_WINE\", \"ALZHEIMERS\", \"VIOSCREEN_SRVID\", \"VIOSCREEN_LINE_GI\", \"VIOSCREEN_TGRAIN\", \"SAMPLE_TYPE\", \"NON_FOOD_ALLERGIES_DRUG_EG_PENICILLIN\", \"MENTAL_ILLNESS_TYPE_ANOREXIA_NERVOSA\", \"SUGAR_SWEETENED_DRINK_FREQUENCY\", \"VIOSCREEN_SUCRLOSE\", \"ENV_BIOME\", \"VIOSCREEN_M_SOY\", \"VIOSCREEN_SUCPOLY\", \"PETS_OTHER_FREETEXT\", \"CONSUME_ANIMAL_PRODUCTS_ABX\", \"VIOSCREEN_ALANINE\", \"VIOSCREEN_CARBO\", \"VIOSCREEN_MFA181\", \"VIOSCREEN_M_FISH_HI\", \"VIOSCREEN_TFA181T\", \"ENV_MATTER\", \"VIOSCREEN_VITD3\", \"VIOSCREEN_ACESUPOT\", \"VIOSCREEN_PROCDATE\", \"VIOSCREEN_GLUTAMIC\", \"VIOSCREEN_HEI2010_SEA_FOODS_PLANT_PROTIENS\", \"VIOSCREEN_SODIUM\", \"ACNE_MEDICATION\", \"VIOSCREEN_THIAMIN\", \"EPILEPSY_OR_SEIZURE_DISORDER\", \"MILK_CHEESE_FREQUENCY\", \"VIOSCREEN_ASPARTAM\", \"ALCOHOL_TYPES_BEERCIDER\", \"VIOSCREEN_VITD_IU\", \"ANTIBIOTIC_HISTORY\", \"HIGH_FAT_RED_MEAT_FREQUENCY\", \"PHYSICAL_SPECIMEN_REMAINING\", \"VIOSCREEN_USER_ID\", \"VIOSCREEN_DOB\", \"VIOSCREEN_HEI_DRK_G_ORG_VEG_LEG\", \"VIOSCREEN_INOSITOL\", \"SOFTENER\", \"VIOSCREEN_FRIED_FISH_SERVINGS\", \"VIOSCREEN_VITB12\", \"VIOSCREEN_SFA40\", \"BODY_HABITAT\", \"VIOSCREEN_TIME\", \"VIOSCREEN_VITE_IU\", \"APPENDIX_REMOVED\", \"DRINKING_WATER_SOURCE\", \"VIOSCREEN_VITA_RAE\", \"BMI_CORRECTED\", \"DIABETES_TYPE\", \"BMI_CAT\", \"VIOSCREEN_MANGAN\", \"VIOSCREEN_PROTVEG\", \"DIET_TYPE\", \"RED_MEAT_FREQUENCY\", \"AUTOIMMUNE\", \"BIRTH_YEAR\", \"VIOSCREEN_AGE\", \"VIOSCREEN_GLYCITN\", \"VIOSCREEN_SCF\", \"VIOSCREEN_GLYCINE\", \"ALCOHOL_CONSUMPTION\", \"Description\", \"VIOSCREEN_LACTOSE\", \"VIOSCREEN_VITB6\", \"MEAT_EGGS_FREQUENCY\", \"VIOSCREEN_D_CHEESE\", \"VIOSCREEN_NCCGLBR\", \"VIOSCREEN_HEI2010_GREENS_BEANS\", \"VIOSCREEN_CAFFEINE\", \"VIOSCREEN_DAIDZEIN\", \"VIOSCREEN_NITROGEN\", \"VIOSCREEN_SERINE\", \"VIOSCREEN_PFA204\", \"VIOSCREEN_PFA205\", \"VIOSCREEN_G_NWHL\", \"VIOSCREEN_MALTOSE\", \"LATITUDE\", \"VEGETABLE_FREQUENCY\", \"VIOSCREEN_HEI_OILS\", \"VIOSCREEN_JOULES\", \"VIOSCREEN_FORMONTN\", \"VIOSCREEN_SWEET_SERVINGS\", \"VIOSCREEN_CHOLEST\", \"POOL_FREQUENCY\", \"PKU\", \"STATE\", \"VIOSCREEN_METHHIS3\", \"AGE_CORRECTED\", \"MENTAL_ILLNESS_TYPE_UNSPECIFIED\", \"VIOSCREEN_MULTIVITAMIN_FREQ\", \"VIOSCREEN_NATOCO\", \"SIMPLE_BODY_SITE\", \"TITLE_ACRONYM\", \"TITLE_BODY_SITE\", \"HMP_SITE\", \"ExtractionKit_lot\", \"Extraction_robot\", \"MasterMix_lot\", \"Orig_name\", \"PlateID\", \"Plating\", \"PrimerPlate\", \"Primer_Plate\", \"Primer_date\", \"Processing_robot\", \"Project_name\", \"Sample_Plate\", \"TM1000_8_tool\", \"TM300_8_tool\", \"TM50_8_tool\", \"Water_Lot\", \"Well\", \"Well_ID\", \"barcode\", \"center_name\", \"center_project_name\", \"experiment_center\", \"experiment_design_description\", \"experiment_title\", \"instrument_model\", \"library_construction_protocol\", \"linker\", \"orig_name\", \"pcr_primers\", \"platform\", \"primer\", \"run_center\", \"run_date\", \"run_prefix\", \"samp_size\", \"sample_type\", \"sequencing_meth\", \"target_gene\", \"target_subfragment\", \"well_description\", \"bloom_counts\", \"nonbloom_counts\", \"viable\"],\n",
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