Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "013641"
$split = "___"
$target = array(
"Target" => array(
"id" => "14070",
"target_id" => "013641",
"local_target_id" => "013641",
"locus_tag" => "KPK_1267",
"ncbi_gi" => "206579197",
"ncbi_accession" => "YP_002237127.1",
"ncbi_geneid" => "6935801",
"ncbi_taxon_id" => "507522",
"gene_name" => null,
"common_name" => "hypothetical protein KPK_1267 [Klebsiella pneumoniae 342]",
"ncbi_coded_by_region" => "complement(NC_011283.1:1284219..1284869)",
"ncbi_note" => "identified by similarity to GB:AAV76351.1",
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => "Symbiotic and global nitrogen fixation based on ortholog expansion from Sinorhizobium",
"sequence" => "MAFSLPDLMDVVHKYNRNPTPKPMPVDEVDRLRVRKYRDPQNSETVALPESLKALLVYDCQLKSPHGQLVLEWVVDSIDEHGVLLSDSLDEDAYYMNGLDMAGLDFEELMPVWNDDPRLPALIRISHAGDQQVFIYVTERDEQGEYPVVRFEGKENDLWLAESSLIEYLQGIFAGSEESHDEWQHQQTLNEARDGALLELEYIHEDLYARLEGCPD",
"sequence_length" => "216",
"dna_sequence" => "ATGGCATTTTCATTACCGGATCTCATGGATGTCGTACATAAGTACAACCGCAATCCCACCCCGAAACCGATGCCCGTAGACGAAGTGGATCGCCTGCGGGTACGGAAATATCGTGACCCGCAAAATAGCGAAACCGTGGCGCTTCCGGAGAGTCTGAAAGCGCTGTTGGTCTACGATTGCCAACTGAAAAGCCCCCACGGACAGCTGGTACTGGAATGGGTTGTGGACTCCATTGATGAACATGGCGTCCTGCTTTCCGACTCGCTGGATGAAGATGCTTATTACATGAATGGTCTTGATATGGCCGGACTGGACTTTGAAGAGCTGATGCCCGTCTGGAACGACGATCCGCGTCTTCCTGCCCTGATTCGCATCAGCCACGCCGGCGATCAGCAGGTATTTATCTATGTCACTGAACGTGATGAACAAGGTGAATATCCTGTTGTCCGCTTCGAGGGTAAAGAGAATGATCTCTGGCTGGCAGAATCGTCACTGATTGAATATCTGCAGGGGATCTTTGCCGGCAGCGAGGAGAGTCACGACGAATGGCAGCATCAGCAGACCCTCAATGAGGCACGCGATGGCGCCTTGCTGGAGCTGGAATATATTCATGAGGATCTTTACGCCAGGCTCGAAGGCTGTCCTGACTAA",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "BIO:N2F",
"selection_phase" => null,
"date_selected" => "2011-09-26",
"date_approved" => "2011-09-26",
"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" => "2011-10-05 19:40:34.411043+00",
"updated" => "2011-10-05 19:40:34.411043+00",
"species_taxon_id" => "573",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "in_crystallization_trials",
"hidden" => false,
"submitter_id" => null,
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => "N2F 2011-09-30",
"genus_taxon_id" => "570",
"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" => 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___013641"
),
array(
"Target___013641",
"ProteinClone___55944"
),
array(
"Target___013641",
"ProteinClone___55944",
"Expression___7394"
)
)
$tips = array(
"Target___013641" => array(
"title" => "Target 013641",
"text" => "hypothetical protein KPK_1267 [Klebsiella pneumoniae 342]"
),
"ProteinClone___55944" => array(
"title" => "Clone",
"text" => "sequence range: 1-216<br>vector: pSGC-His<br>person: Brandan Hillerich"
),
"Expression___7394" => array(
"title" => "Expression",
"text" => "expression level: 100.0%<br>solubility level: 66.7%<br>media: PASM-SEMET (2000mL)<br>induction: IPTG (37°C)<br>person: James Hammonds"
),
"Purification___2135" => array(
"title" => "Purification",
"text" => "final concentration: 1.8248mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Nawar Al"
)
)
$root = array(
"id" => "Target___013641",
"name" => "T 013641",
"data" => array()
)
$clones = array()
$sclone = array(
"id" => "55944",
"target_id" => "013641",
"clone_suffix" => "11157",
"sequence_start" => "1",
"sequence_end" => "216",
"sequence" => "MHHHHHHSSGVDLGTENLYFQSMAFSLPDLMDVVHKYNRNPTPKPMPVDEVDRLRVRKYRDPQNSETVALPESLKALLVYDCQLKSPHGQLVLEWVVDSIDEHGVLLSDSLDEDAYYMNGLDMAGLDFEELMPVWNDDPRLPALIRISHAGDQQVFIYVTERDEQGEYPVVRFEGKENDLWLAESSLIEYLQGIFAGSEESHDEWQHQQTLNEARDGALLELEYIHEDLYARLEGCPD",
"sequence_comments" => null,
"local_protein_target_id" => "15015",
"local_clone_plate_id" => null,
"local_clone_id" => "11157",
"experiment_date_start" => "2011-11-04",
"experiment_date_end" => "2011-11-04",
"staff_id" => "23",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pSGC-His",
"pcr_primer_forward" => "TACTTCCAATCCATGGCATTTTCATTACCGGATCTCATGG",
"pcr_primer_backward" => "TATCCACCTTTACTGTTAGTCAGGACAGCCTTCGAGC",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2011-11-04 14:02:36.870612+00",
"ins_user_id" => null,
"update" => "2014-05-20 02:01:48.800067+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" => "ATGCACCATCATCATCATCATTCTTCTGGTGTAGATCTGGGTACCGAGAACCTGTACTTCCAATCCATGGCATTTTCATTACCGGATCTCATGGATGTCGTACATAAGTACAACCGCAATCCCACCCCGAAACCGATGCCCGTAGACGAAGTGGATCGCCTGCGGGTACGGAAATATCGTGACCCGCAAAATAGCGAAACCGTGGCGCTTCCGGAGAGTCTGAAAGCGCTGTTGGTCTACGATTGCCAACTGAAAAGCCCCCACGGACAGCTGGTACTGGAATGGGTTGTGGACTCCATTGATGAACATGGCGTCCTGCTTTCCGACTCGCTGGATGAAGATGCTTATTACATGAATGGTCTTGATATGGCCGGACTGGACTTTGAAGAGCTGATGCCCGTCTGGAACGACGATCCGCGTCTTCCTGCCCTGATTCGCATCAGCCACGCCGGCGATCAGCAGGTATTTATCTATGTCACTGAACGTGATGAACAAGGTGAATATCCTGTTGTCCGCTTCGAGGGTAAAGAGAATGATCTCTGGCTGGCAGAATCGTCACTGATTGAATATCTGCAGGGGATCTTTGCCGGCAGCGAGGAGAGTCACGACGAATGGCAGCATCAGCAGACCCTCAATGAGGCACGCGATGGCGCCTTGCTGGAGCTGGAATATATTCATGAGGATCTTTACGCCAGGCTCGAAGGCTGTCCTGAC",
"lims_date" => "2011-11-04",
"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___55944",
"name" => "C .11/04/11",
"data" => array(),
"children" => array()
)
$sexpr = array(
"id" => "7394",
"target_id" => "013641",
"expression_suffix" => "9973",
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"local_expression_id" => "9973",
"experiment_date_start" => "2011-11-23",
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"staff_id" => "216",
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"protocol_id" => "LEX48 PASM-5052 Large Scale Expression",
"status" => "success",
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"expression_strain" => "BL21 (DE3) RIL",
"media_type" => "PASM-SEMET",
"media_volume" => "2000",
"growth_temperature" => "37",
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"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => "100",
"solubility_level" => "66.6667",
"inserted" => "2011-12-07 18:06:35.274462+00",
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"update" => "2014-05-19 02:15:21.001748+00",
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array(),
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"name" => "E .11/23/11",
"data" => array(),
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"status" => "success",
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"affinity_tag_status" => "na",
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array()
),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___2135",
"name" => "P .12/12/11"
)
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