Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "012903"
$split = "___"
$target = array(
"Target" => array(
"id" => "13332",
"target_id" => "012903",
"local_target_id" => "012903",
"locus_tag" => "SIAM614_28497",
"ncbi_gi" => "118591613",
"ncbi_accession" => "ZP_01549010.1",
"ncbi_geneid" => null,
"ncbi_taxon_id" => "384765",
"gene_name" => null,
"common_name" => "muconate lactonizing enzyme [Stappia aggregata IAM 12614]",
"ncbi_coded_by_region" => "NZ_AAUW01000014.1:182360..183463",
"ncbi_note" => "COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily",
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => "Community target program on mechanistically diverse enzyme superfamilies",
"sequence" => "MKITAINVFQVDLPLREGRYSWSNGNFVEVFDSTVVEIETDEGLKGYAECCPLGSAYLPSYALGVRSGLQELAPHLIGKDPLNIGEINRVMDAALRGHPYAKAPIDIACWDLLGKATGQPLYTLLGGAAQDDVALYRAISQEAPEIMAKKIEGYAAEGYTKFQLKVGGDANDDINRIHATRSVLKKSDLLVADANTGWTRHEAARVVGAVSSLDVYIEQPCLTYEESVSIRRRTALPFVLDEVIDGPNTLVRGIAEDAMDCINLKISKVGGLTKAKLMRDLCIAHGIPMTIEDTWGGDIVTAAIAHLARSTPSEFTFSATDFNSYGTVDIAEGAPKRVNGRMTTSDLPGLGITPIFDVLGEPVARYS",
"sequence_length" => "367",
"dna_sequence" => "ATGGCGCGCAAAAGCTCCGCTCCGCAATTCCTGTCCTACGGGGACGCGACAGGCCGGCTAAGCTGGCGCGATGCCGTCGAGGCGCTGCGCCAGGGCCACACCCTGCCGCAGGCCCAGATCAGGGACGTGTTCCTTGGCCCGCCCACCGGCACGATGATGAGCCGCTCGGCCTGGATCGAGGGGCTGGGCTACGGCGCCAAGACCTTCACCGTCTTCGACGGCAATGCGGCACGCGGCCTTCCGACAGTGCAGGGCGCCATGCTGGTCTTCGACAAGGATGACGGCCGGCTGCAAGCCATCGTGGACAGCCCGCTGGTCACCGAATTCAAGACCGCCGCCGATTCCGTCCTGGGCGCAAGCCTGCTTGCGCGACCGGACAGCCGGCATCTGCTGATCGTCGGTGCGGGGACGGTCGCGGCCAGCCTTGTGCGGGCCTATACGGCGGTGCTGCCGGGGATCGAGCGCGTCTCGGTCTGGGCCCGCCGCCCGCAGCAGGCGCAGGATCTGATCGAAGGGCTGGACGGCATCGAGGCGGATCTGGCCGCGGTCAGCGATCTGCCGGCCGCGGTGGGGCAGGCCGACATCGTCTCTTCGGCCACCATGGCGCGGCAGCCGGTGATCCTGGGCGCCTGGGTGCGGCCCGGCACCCATGTCGACCTGATCGGCGCCTTCAAGGCCGACATGCGCGAGGCCGACGATGCGCTGATGGCAAGGGCCGCGCTGTTCGTGGACAGCCGCGAGACCACGCTGGGCCATATCGGCGAGCTGATGCTGCCCATCGCCTCGGGCGCGATCACCGCCGAAAGCGTGCTGGGCGATCTCTATGATCTCGTGCGTCCCGGTGCCCGCCGGCGGCAATCGGAGGACGAGATTACCGTGTTCAAGAACGGCGGCGGCGCGCATCTGGACCTGATGATCGCGTCCTACATTGCGCGCGTGATGGCGGGGTAG",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "COM (Community Requests)",
"selection_phase" => null,
"date_selected" => "2011-09-22",
"date_approved" => "2011-09-22",
"completion_code" => null,
"pi" => null,
"tms" => null,
"sp" => null,
"core_genome" => null,
"gram_minus_gene_homolog" => null,
"gram_plus_gene_homolog" => null,
"protease_motifs" => null,
"glycosyl_group_metabolism" => null,
"study_id" => null,
"drug_target_homologs" => null,
"virulence_genes" => null,
"essential_genes_homologs" => null,
"dna_binding_motifs" => null,
"inserted" => "2011-09-22 16:45:22.140614+00",
"updated" => "2011-09-22 16:45:22.140614+00",
"species_taxon_id" => "187304",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "in_crystallization_trials",
"hidden" => false,
"submitter_id" => "212",
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => "COM batch 2",
"genus_taxon_id" => "478070",
"seguid" => null,
"uniprot_id" => null,
"ec" => null,
"target_family" => null,
"tar_designpool_id" => null,
"community_nominated" => true,
"partnership_nominated" => null,
"biomedical" => false,
"metagenomic" => false,
"structural_coverage" => false,
"psi2" => false,
"legacy" => false,
"complex_with_biological_partner" => false,
"functional_mutant" => false,
"conformational_state" => false,
"disease" => false,
"individual_organism" => false,
"protein_family_of_high_biological_importance" => false,
"general_domain_family" => false,
"eukaryotic_domain_family" => false,
"first_structure_of_class" => false,
"functional_follow_up" => false,
"technology_development" => false,
"membrane_protein" => false,
"translated_dna_sequence" => null,
"family_coverage" => null,
"family_coverage_date" => null,
"distribution_lab" => null,
"uniprot_accession" => null,
"protocol_id" => "Target_selection",
"ensembl_protein_id" => null,
"ensembl_gene_id" => null,
"type" => "single protein",
"ligand_studies" => false,
"protein_production_for_partnerships" => false,
"single_domain_protein" => false,
"multidomain_protein" => false,
"oligomeric_protein" => false,
"eukaryotic_protein" => false,
"protein_protein_complex" => false,
"protein_nucleic_acid_complex" => false,
"protein_ligand_complex" => false,
"de_novo_designed_protein" => false,
"post_translational_modification" => false
),
"ProteinClone" => array(
array(),
array()
)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___012903"
),
array(
"Target___012903",
"ProteinClone___54885"
),
array(
"Target___012903",
"ProteinClone___54885",
"Expression___5879"
)
)
$tips = array(
"Target___012903" => array(
"title" => "Target 012903",
"text" => "muconate lactonizing enzyme [Stappia aggregata IAM 12614]"
),
"ProteinClone___54885" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pSGC-His<br>person: Brandan Hillerich"
),
"Expression___5879" => array(
"title" => "Expression",
"text" => "expression level: 66.7%<br>solubility level: 66.7%<br>media: PASM-SEMET (2000mL)<br>induction: IPTG (37°C)<br>person: James Hammonds"
),
"Purification___1595" => array(
"title" => "Purification",
"text" => "final concentration: 0.3647mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Alan Glenn"
)
)
$root = array(
"id" => "Target___012903",
"name" => "T 012903",
"data" => array()
)
$clones = array()
$sclone = array(
"id" => "54885",
"target_id" => "012903",
"clone_suffix" => "9785",
"sequence_start" => "0",
"sequence_end" => "0",
"sequence" => "KITAINVFQVDLPLREGRYSWSNGNFVEVFDSTVVEIETDEGLKGYAECCPLGSAYLPSYALGVRSGLQELAPHLIGKDPLNIGEINRVMDAALRGHPYAKAPIDIACWDLLGKATGQPLYTLLGGAAQDDVALYRAISQEAPEIMAKKIEGYAAEGYTKFQLKVGGDANDDINRIHATRSVLKKSDLLVADANTGWTRHEAARVVGAVSSLDVYIEQPCLTYEESVSIRRRTALPFVLDEVIDGPNTLVRGIAEDAMDCINLKISKVGGLTKAKLMRDLCIAHGIPMTIEDTWGGDIVTAAIAHLARSTPSEFTFSATDFNSYGTVDIAEGAPKRVNGRMTTSDLPGLGITPIFDVLGEPVARYS",
"sequence_comments" => null,
"local_protein_target_id" => "14181",
"local_clone_plate_id" => null,
"local_clone_id" => "9785",
"experiment_date_start" => "2011-10-07",
"experiment_date_end" => "2011-10-07",
"staff_id" => "23",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pSGC-His",
"pcr_primer_forward" => "TACTTCCAATCCATGAAAATCACCGCCATCAATGTCTTTCAG",
"pcr_primer_backward" => "TATCCACCTTTACTGTTAAGAGTAACGTGCCACCGGTTC",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2011-10-11 16:38:08.885728+00",
"ins_user_id" => null,
"update" => "2014-05-20 02:01:33.357402+00",
"upd_user_id" => "1",
"secondary_shipped_to_lab_id" => null,
"secondary_shipped_date" => null,
"external_source" => false,
"mutation" => null,
"bei_available" => false,
"bei_number" => null,
"reference_sequence_variance" => null,
"confirmed_dna_sequence" => null,
"confirmed_protein_sequence" => null,
"present_in_lims" => false,
"template_dna_sequence" => "AAAATCACCGCCATCAATGTCTTTCAGGTCGATCTGCCGCTGCGCGAAGGCCGCTATTCTTGGAGCAACGGTAACTTTGTGGAAGTGTTTGATAGTACCGTGGTTGAAATCGAAACGGACGAAGGCCTGAAAGGTTATGCAGAATGCTGTCCGCTGGGTAGCGCGTATCTGCCGTCTTACGCACTGGGTGTTCGTAGCGGTCTGCAAGAACTGGCCCCGCATCTGATTGGCAAAGATCCGCTGAACATTGGTGAAATCAATCGTGTCATGGATGCAGCACTGCGTGGTCACCCGTATGCAAAAGCTCCGATTGATATCGCATGCTGGGACCTGCTGGGCAAAGCTACCGGTCAGCCGCTGTATACGCTGCTGGGCGGTGCAGCTCAAGATGACGTGGCGCTGTACCGTGCCATCTCTCAGGAAGCACCGGAAATCATGGCGAAGAAAATTGAAGGCTATGCGGCCGAAGGTTACACCAAATTTCAACTGAAAGTTGGCGGTGATGCGAACGATGACATTAATCGCATCCATGCCACGCGTAGTGTTCTGAAAAAATCCGATCTGCTGGTCGCGGACGCAAACACCGGTTGGACGCGTCACGAAGCAGCTCGTGTCGTGGGTGCCGTGAGCTCTCTGGATGTTTATATCGAACAGCCGTGTCTGACCTACGAAGAAAGTGTGTCCATTCGTCGCCGTACGGCCCTGCCGTTCGTTCTGGATGAAGTCATCGACGGTCCGAACACCCTGGTCCGTGGTATTGCAGAAGATGCTATGGACTGCATTAATCTGAAAATCAGCAAAGTGGGCGGTCTGACCAAAGCAAAACTGATGCGTGATCTGTGTATTGCTCATGGTATCCCGATGACCATTGAAGATACGTGGGGCGGTGACATCGTTACCGCAGCAATTGCACACCTGGCACGTTCAACGCCGTCGGAATTTACCTTCTCAGCGACGGATTTTAACTCGTATGGCACCGTGGACATTGCAGAAGGTGCTCCGAAACGCGTTAATGGCCGTATGACCACGAGCGATCTGCCGGGCCTGGGTATTACCCCGATCTTCGACGTCCTGGGTGAACCGGTGGCACGTTACTCT",
"lims_date" => "2011-10-11",
"dummy" => false,
"type" => null,
"clone_annotation" => null,
"optimized_dna_sequence" => null,
"optimized" => false,
"truncated" => false,
"synthetic" => false,
"Staff" => array(
"id" => "23",
"first_name" => "Brandan",
"last_name" => "Hillerich",
"email" => "brandan.hillerich@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2010-11-16 22:19:15.566353+00",
"updated" => "2010-11-16 22:19:15.566353+00",
"institution_id" => "1",
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "23"
),
"Expression" => array(
array(),
array(),
array()
)
)
$iclone = array(
"id" => "ProteinClone___54885",
"name" => "C .10/07/11",
"data" => array(),
"children" => array()
)
$sexpr = array(
"id" => "5879",
"target_id" => "012903",
"expression_suffix" => "8364",
"clone_id" => "54885",
"clone_suffix" => "9785",
"local_clone_id" => "9785",
"local_protein_target_id" => "14181",
"local_expression_id" => "8364",
"experiment_date_start" => "2011-10-19",
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"staff_id" => "216",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "LEX48 PASM-5052 Large Scale Expression",
"status" => "success",
"expression_organism" => "E. coli",
"expression_strain" => "BL21 (DE3) RIL",
"media_type" => "PASM-SEMET",
"media_volume" => "2000",
"growth_temperature" => "37",
"induction_temperature" => "37",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => "66.6667",
"solubility_level" => "66.6667",
"inserted" => "2011-10-24 21:05:04.341444+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:14:47.756186+00",
"upd_user_id" => "1",
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"dummy" => false,
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"first_name" => "James",
"last_name" => "Hammonds",
"email" => "james.hammonds@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2010-12-16 18:46:05.227363+00",
"updated" => "2010-12-16 18:46:05.227363+00",
"institution_id" => "1",
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"active" => true,
"manager" => false,
"function" => null,
"real_id" => "216"
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___5879",
"name" => "E .10/19/11",
"data" => array(),
"children" => array()
)
$expression_level = "66.7%"
$solubility_level = "66.7%"
$spur = array(
"id" => "1595",
"target_id" => "012903",
"purification_suffix" => "1604",
"expression_id" => "5879",
"local_expression_id" => "8364",
"local_protein_target_id" => "14181",
"local_purification_id" => "1604",
"experiment_date_start" => "2011-10-25",
"experiment_date_end" => "2011-10-26",
"staff_id" => "429",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large-Scale Automated Protein Purification",
"status" => "success",
"description" => "",
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => "",
"final_concentration" => "0.3647",
"final_volume" => "6069.2",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2011-10-30 14:05:26.095414+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:28:44.88731+00",
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"yield" => null,
"Staff" => array(
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"first_name" => "Alan",
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"email" => "alan.glenn@einstein.yu.edu",
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"databases" => false,
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"pi" => false,
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"inserted" => "2012-02-11 15:00:14.66753+00",
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$ipur = array(
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"name" => "P .10/25/11"
)
Unitrack_SpaceTreeController::create_JSON() - /var/www/unitrack/controllers/unitrack_space_tree_controller.php, line 205
Unitrack_SpaceTreeController::view() - /var/www/unitrack/controllers/unitrack_space_tree_controller.php, line 48
Dispatcher::_invoke() - CORE/cake/dispatcher.php, line 204
Dispatcher::dispatch() - CORE/cake/dispatcher.php, line 171
[main] - APP/webroot/index.php, line 83