Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "030801"
$split = "___"
$target = array(
"Target" => array(
"id" => "33015",
"target_id" => "030801",
"local_target_id" => "030801",
"locus_tag" => "BF1380",
"ncbi_gi" => "60680894",
"ncbi_accession" => "YP_211038.1",
"ncbi_geneid" => "3289409",
"ncbi_taxon_id" => "272559",
"gene_name" => null,
"common_name" => "methyltransferase [Bacteroides fragilis NCTC 9343]",
"ncbi_coded_by_region" => "complement(NC_003228.3:1648522..1649301)",
"ncbi_note" => null,
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => null,
"sequence" => "MNSLSLPAVTTKNQSMNTSLLPAEKDPMGAAIADFYHRQKADRLRVFSSQFDEDEIPVKQLFRKAGQMPLLERTALAMATGTILDVGAGSGCHALALQESGKEVSAIDISPLSVEVMKLRGVKDARQVNLFDERFAATFDTILMLMNGSGIIGRLENMPLFFRKMKQLLRPDGCILMDSSDLRYLFEDEDGSFLIDLAGDYYGEIDFRMQYKDIQGDPFDWLYIDFQTLSAYAADNGFKAEMIKEGKHYDYLARLTVAL",
"sequence_length" => "259",
"dna_sequence" => "GTGAATTCCCTATCTTTGCCCGCTGTAACAACTAAAAACCAATCAATGAATACATCCCTGCTCCCGGCAGAAAAAGACCCCATGGGTGCTGCCATAGCCGATTTTTATCATCGCCAAAAAGCAGACAGATTACGCGTATTTTCTTCTCAGTTCGATGAAGACGAAATACCCGTCAAACAACTTTTCCGCAAAGCCGGACAAATGCCTCTACTCGAACGCACAGCCCTCGCAATGGCTACCGGAACAATACTCGACGTAGGTGCCGGAAGCGGTTGCCACGCTCTTGCCCTTCAAGAGAGCGGTAAAGAAGTTTCCGCCATCGACATCTCCCCTTTATCCGTCGAAGTGATGAAACTGCGGGGAGTGAAAGATGCCCGCCAAGTCAATCTGTTCGACGAACGCTTTGCCGCGACTTTCGATACCATCCTTATGTTGATGAACGGTTCCGGCATTATCGGACGTTTGGAGAATATGCCTCTCTTCTTCCGCAAGATGAAACAATTACTCCGCCCGGATGGTTGCATCCTGATGGATTCGAGTGACCTCCGCTATCTGTTCGAAGATGAAGACGGCAGCTTCCTGATCGACCTGGCAGGAGATTATTATGGAGAAATTGACTTCCGCATGCAATATAAAGATATTCAAGGCGATCCTTTCGACTGGCTGTATATCGACTTCCAGACCCTCAGCGCCTATGCTGCCGACAATGGCTTCAAGGCCGAAATGATAAAAGAGGGTAAGCACTATGACTATCTGGCCCGGCTGACTGTTGCCTTATAA",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "BIO:P18",
"selection_phase" => null,
"date_selected" => "2012-12-21",
"date_approved" => "2012-12-21",
"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" => "2013-01-07 18:18:25.989783+00",
"updated" => "2013-01-07 18:18:25.989783+00",
"species_taxon_id" => "817",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "in_pdb",
"hidden" => false,
"submitter_id" => null,
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => "p18",
"genus_taxon_id" => "816",
"seguid" => null,
"uniprot_id" => null,
"ec" => null,
"target_family" => null,
"tar_designpool_id" => null,
"community_nominated" => false,
"partnership_nominated" => null,
"biomedical" => true,
"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" => "VNSLSLPAVTTKNQSMNTSLLPAEKDPMGAAIADFYHRQKADRLRVFSSQFDEDEIPVKQLFRKAGQMPLLERTALAMATGTILDVGAGSGCHALALQESGKEVSAIDISPLSVEVMKLRGVKDARQVNLFDERFAATFDTILMLMNGSGIIGRLENMPLFFRKMKQLLRPDGCILMDSSDLRYLFEDEDGSFLIDLAGDYYGEIDFRMQYKDIQGDPFDWLYIDFQTLSAYAADNGFKAEMIKEGKHYDYLARLTVAL*",
"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()
)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___030801"
),
array(
"Target___030801",
"ProteinClone___76058"
),
array(
"Target___030801",
"ProteinClone___76058",
"Expression___31928"
),
array(
"Target___030801",
"ProteinClone___76058",
"Expression___32664"
),
array(
"Target___030801",
"ProteinClone___76058",
"Expression___32940"
)
)
$tips = array(
"Target___030801" => array(
"title" => "Target 030801",
"text" => "methyltransferase [Bacteroides fragilis NCTC 9343]"
),
"ProteinClone___76058" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pSGC-His<br>person: Mark Stead"
),
"Expression___31928" => array(
"title" => "Expression",
"text" => "expression level: 100.0%<br>solubility level: 100.0%<br>media: PASM-5052 (0.75mL)<br>induction: IPTG (37°C)<br>person: Mark Stead"
),
"Expression___32664" => 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: Brandan Hillerich"
),
"Expression___32940" => 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: Brandan Hillerich"
),
"Purification___4450" => array(
"title" => "Purification",
"text" => "final concentration: 3.15mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Muftah Ahmed"
)
)
$root = array(
"id" => "Target___030801",
"name" => "T 030801",
"data" => array()
)
$clones = array()
$sclone = array(
"id" => "76058",
"target_id" => "030801",
"clone_suffix" => "35532",
"sequence_start" => "0",
"sequence_end" => "0",
"sequence" => "VNSLSLPAVTTKNQSMNTSLLPAEKDPMGAAIADFYHRQKADRLRVFSSQFDEDEIPVKQLFRKAGQMPLLERTALAMATGTILDVGAGSGCHALALQESGKEVSAIDISPLSVEVMKLRGVKDARQVNLFDERFAATFDTILMLMNGSGIIGRLENMPLFFRKMKQLLRPDGCILMDSSDLRYLFEDEDGSFLIDLAGDYYGEIDFRMQYKDIQGDPFDWLYIDFQTLSAYAADNGFKAEMIKEGKHYDYLARLTVAL",
"sequence_comments" => null,
"local_protein_target_id" => "35356",
"local_clone_plate_id" => null,
"local_clone_id" => "35532",
"experiment_date_start" => "2013-03-05",
"experiment_date_end" => "2013-03-05",
"staff_id" => "430",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pSGC-His",
"pcr_primer_forward" => "TACTTCCAATCCATGGTGAATTCCCTATCTTTGCCCGC",
"pcr_primer_backward" => "TATCCACCTTTACTGTTATAAGGCAACAGTCAGCCGGG",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-03-05 20:01:48.695902+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:07:15.50909+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" => "GTGAATTCCCTATCTTTGCCCGCTGTAACAACTAAAAACCAATCAATGAATACATCCCTGCTCCCGGCAGAAAAAGACCCCATGGGTGCTGCCATAGCCGATTTTTATCATCGCCAAAAAGCAGACAGATTACGCGTATTTTCTTCTCAGTTCGATGAAGACGAAATACCCGTCAAACAACTTTTCCGCAAAGCCGGACAAATGCCTCTACTCGAACGCACAGCCCTCGCAATGGCTACCGGAACAATACTCGACGTAGGTGCCGGAAGCGGTTGCCACGCTCTTGCCCTTCAAGAGAGCGGTAAAGAAGTTTCCGCCATCGACATCTCCCCTTTATCCGTCGAAGTGATGAAACTGCGGGGAGTGAAAGATGCCCGCCAAGTCAATCTGTTCGACGAACGCTTTGCCGCGACTTTCGATACCATCCTTATGTTGATGAACGGTTCCGGCATTATCGGACGTTTGGAGAATATGCCTCTCTTCTTCCGCAAGATGAAACAATTACTCCGCCCGGATGGTTGCATCCTGATGGATTCGAGTGACCTCCGCTATCTGTTCGAAGATGAAGACGGCAGCTTCCTGATCGACCTGGCAGGAGATTATTATGGAGAAATTGACTTCCGCATGCAATATAAAGATATTCAAGGCGATCCTTTCGACTGGCTGTATATCGACTTCCAGACCCTCAGCGCCTATGCTGCCGACAATGGCTTCAAGGCCGAAATGATAAAAGAGGGTAAGCACTATGACTATCTGGCCCGGCTGACTGTTGCCTTA",
"lims_date" => "2013-03-05",
"dummy" => false,
"type" => null,
"clone_annotation" => null,
"optimized_dna_sequence" => null,
"optimized" => false,
"truncated" => false,
"synthetic" => false,
"Staff" => array(
"id" => "430",
"first_name" => "Mark",
"last_name" => "Stead",
"email" => "mark.stead@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" => "2012-02-28 22:00:05.514568+00",
"updated" => "2012-02-28 22:00:05.514568+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "430"
),
"Expression" => array(
array(),
array(),
array(),
array()
)
)
$iclone = array(
"id" => "ProteinClone___76058",
"name" => "C .03/05/13",
"data" => array(),
"children" => array(
array(),
array()
)
)
$sexpr = array(
"id" => "32940",
"target_id" => "030801",
"expression_suffix" => "44974",
"clone_id" => "76058",
"clone_suffix" => "35532",
"local_clone_id" => "35532",
"local_protein_target_id" => "35356",
"local_expression_id" => "44974",
"experiment_date_start" => "2013-04-19",
"experiment_date_end" => "2013-04-19",
"staff_id" => "23",
"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" => "2013-04-25 16:00:26.883862+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:24:31.184705+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-04-25",
"dummy" => 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"
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___32940",
"name" => "E .04/19/13",
"data" => array(),
"children" => array()
)
$expression_level = "66.7%"
$solubility_level = "66.7%"
$spur = array(
"id" => "4450",
"target_id" => "030801",
"purification_suffix" => "5439",
"expression_id" => "32940",
"local_expression_id" => "44974",
"local_protein_target_id" => "35356",
"local_purification_id" => "5439",
"experiment_date_start" => "2013-04-29",
"experiment_date_end" => "2013-04-30",
"staff_id" => "1825",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large-Scale Automated Protein Purification",
"status" => "success",
"description" => null,
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => null,
"final_concentration" => "3.15",
"final_volume" => "10210",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-05-01 17:00:30.19227+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:29:41.887863+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-05-01",
"dummy" => false,
"yield" => null,
"Staff" => array(
"id" => "1825",
"first_name" => "Muftah",
"last_name" => "Ahmed",
"email" => "muftah.ahmed@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" => "2012-06-22 21:00:37.397023+00",
"updated" => "2012-06-22 21:00:37.397023+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "1825"
),
"CrystallizationDrop" => array(),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___4450",
"name" => "P .04/29/13"
)
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
