Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "012320"
$split = "___"
$target = array(
"Target" => array(
"id" => "12382",
"target_id" => "012320",
"local_target_id" => "012320",
"locus_tag" => "SM_b20656",
"ncbi_gi" => "15141250",
"ncbi_accession" => "CAC49763.1",
"ncbi_geneid" => null,
"ncbi_taxon_id" => "266834",
"gene_name" => null,
"common_name" => "putative oxidoreductase protein [Sinorhizobium meliloti 1021]",
"ncbi_coded_by_region" => "AL591985.1:1457321..1458190",
"ncbi_note" => "Hypothetical protein",
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => "Model system for symbiosis and nitrogen fixation",
"sequence" => "MSLPLVPRAWGQAADLTKRVIPKSEEPLPLIGLGTWITFNVGDDPVLMDECAAVIAAFFEGGGRMIDSSPMYGSSQPTIGYGLGKLGYPKQLFSAEKVWISDPGEGAAQIEASKDYWGVRKFDLMQVHNLVSWEEHLPALFDMKAAGRLRYVGITTSEGRRHREIEQIMVSQPIDFVQVTYNILDREVEERILPLAQEKGIAVIVNRPFRQGDLIRQIEDEPLPDWIAETGARSWAQFLLKFIISHPAVTCAIPATTRVDHVRENLEAARGILPDEKLRGRMAAYVEAL",
"sequence_length" => "289",
"dna_sequence" => "ATGTCGCTGCCGCTTGTGCCGCGGGCGTGGGGCCAGGCTGCCGACCTCACGAAGCGGGTCATACCGAAGAGCGAAGAACCGCTGCCGCTCATCGGCCTCGGCACCTGGATCACGTTCAACGTCGGAGACGACCCTGTACTGATGGACGAATGTGCCGCCGTGATCGCTGCCTTCTTCGAAGGCGGCGGTCGCATGATCGATTCCTCGCCGATGTACGGATCGTCCCAGCCGACCATCGGCTACGGCCTCGGCAAGCTCGGATATCCGAAGCAGCTCTTCTCGGCGGAAAAGGTCTGGATATCGGACCCCGGCGAAGGCGCGGCCCAGATCGAAGCATCGAAGGACTACTGGGGCGTCAGAAAATTCGATCTCATGCAGGTTCACAATCTCGTCTCCTGGGAGGAGCACCTGCCCGCGCTCTTCGACATGAAGGCGGCAGGCCGGCTGCGCTATGTCGGCATCACCACCTCGGAGGGGCGCAGGCACCGGGAGATCGAGCAGATCATGGTGAGCCAGCCGATCGATTTCGTCCAGGTCACCTACAATATCCTCGACCGCGAGGTGGAGGAGCGCATCTTGCCGCTGGCGCAGGAGAAGGGCATTGCCGTGATCGTCAACCGGCCGTTCCGGCAGGGCGATCTGATCCGGCAGATTGAAGACGAACCGTTGCCGGACTGGATTGCGGAGACCGGCGCTCGCAGCTGGGCGCAGTTTCTCCTGAAGTTCATCATTTCGCATCCGGCGGTCACCTGCGCAATCCCGGCGACGACGCGCGTCGACCACGTACGGGAGAATCTGGAGGCCGCAAGAGGCATCCTGCCCGACGAGAAGCTGCGCGGACGCATGGCCGCCTATGTGGAGGCGCTCTGA",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "BIO:SINO (Sinorhizobium targets)",
"selection_phase" => null,
"date_selected" => "2011-06-29",
"date_approved" => "2011-06-29",
"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" => "2011-06-29 19:39:10.531802+00",
"updated" => "2011-06-29 19:39:10.531802+00",
"species_taxon_id" => "382",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "diffraction",
"hidden" => false,
"submitter_id" => null,
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => "sinorizobium_batch1",
"genus_taxon_id" => "28105",
"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()
)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___012320"
),
array(
"Target___012320",
"ProteinClone___37219"
),
array(
"Target___012320",
"ProteinClone___37219",
"Expression___61789"
)
)
$tips = array(
"Target___012320" => array(
"title" => "Target 012320",
"text" => "putative oxidoreductase protein [Sinorhizobium meliloti 1021]"
),
"ProteinClone___37219" => array(
"title" => "Clone",
"text" => "sequence range: 1-289<br>vector: pSGC<br>person: Brandan Hillerich"
),
"Expression___61789" => array(
"title" => "Expression",
"text" => "expression level: N/A<br>solubility level: N/A<br>media: LB (2000mL)<br>induction: IPTG (17°C)<br>person: Piotr Sroka"
),
"Purification___5719" => array(
"title" => "Purification",
"text" => "final concentration: 4.07mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Piotr Sroka"
)
)
$root = array(
"id" => "Target___012320",
"name" => "T 012320",
"data" => array()
)
$clones = array()
$sclone = array(
"id" => "37219",
"target_id" => "012320",
"clone_suffix" => "8286",
"sequence_start" => "1",
"sequence_end" => "289",
"sequence" => "MSLPLVPRAWGQAADLTKRVIPKSEEPLPLIGLGTWITFNVGDDPVLMDECAAVIAAFFEGGGRMIDSSPMYGSSQPTIGYGLGKLGYPKQLFSAEKVWISDPGEGAAQIEASKDYWGVRKFDLMQVHNLVSWEEHLPALFDMKAAGRLRYVGITTSEGRRHREIEQIMVSQPIDFVQVTYNILDREVEERILPLAQEKGIAVIVNRPFRQGDLIRQIEDEPLPDWIAETGARSWAQFLLKFIISHPAVTCAIPATTRVDHVRENLEAARGILPDEKLRGRMAAYVEAL*",
"sequence_comments" => null,
"local_protein_target_id" => "12599",
"local_clone_plate_id" => null,
"local_clone_id" => "8286",
"experiment_date_start" => "2011-08-12",
"experiment_date_end" => "2011-08-12",
"staff_id" => "23",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pSGC",
"pcr_primer_forward" => "TACTTCCAATCCATGATGTCGCTGCCGCTTGTGCC",
"pcr_primer_backward" => "tatccacctttactgttaGAGCGCCTCCACATAGGCGG",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2011-08-12 21:02:28.950837+00",
"ins_user_id" => null,
"update" => "2014-05-20 02:01:23.353426+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" => "ATGTCGCTGCCGCTTGTGCCGCGGGCGTGGGGCCAGGCTGCCGACCTCACGAAGCGGGTCATACCGAAGAGCGAAGAACCGCTGCCGCTCATCGGCCTCGGCACCTGGATCACGTTCAACGTCGGAGACGACCCTGTACTGATGGACGAATGTGCCGCCGTGATCGCTGCCTTCTTCGAAGGCGGCGGTCGCATGATCGATTCCTCGCCGATGTACGGATCGTCCCAGCCGACCATCGGCTACGGCCTCGGCAAGCTCGGATATCCGAAGCAGCTCTTCTCGGCGGAAAAGGTCTGGATATCGGACCCCGGCGAAGGCGCGGCCCAGATCGAAGCATCGAAGGACTACTGGGGCGTCAGAAAATTCGATCTCATGCAGGTTCACAATCTCGTCTCCTGGGAGGAGCACCTGCCCGCGCTCTTCGACATGAAGGCGGCAGGCCGGCTGCGCTATGTCGGCATCACCACCTCGGAGGGGCGCAGGCACCGGGAGATCGAGCAGATCATGGTGAGCCAGCCGATCGATTTCGTCCAGGTCACCTACAATATCCTCGACCGCGAGGTGGAGGAGCGCATCTTGCCGCTGGCGCAGGAGAAGGGCATTGCCGTGATCGTCAACCGGCCGTTCCGGCAGGGCGATCTGATCCGGCAGATTGAAGACGAACCGTTGCCGGACTGGATTGCGGAGACCGGCGCTCGCAGCTGGGCGCAGTTTCTCCTGAAGTTCATCATTTCGCATCCGGCGGTCACCTGCGCAATCCCGGCGACGACGCGCGTCGACCACGTACGGGAGAATCTGGAGGCCGCAAGAGGCATCCTGCCCGACGAGAAGCTGCGCGGACGCATGGCCGCCTATGTGGAGGCGCTCTGA",
"lims_date" => "2011-08-12",
"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(),
array(),
array(),
array()
)
)
$iclone = array(
"id" => "ProteinClone___37219",
"name" => "C .08/12/11",
"data" => array(),
"children" => array()
)
$sexpr = array(
"id" => "61789",
"target_id" => "012320",
"expression_suffix" => "702",
"clone_id" => "37219",
"clone_suffix" => "8286",
"local_clone_id" => "-9",
"local_protein_target_id" => "1679",
"local_expression_id" => "702",
"experiment_date_start" => "2015-03-09",
"experiment_date_end" => "2015-03-10",
"staff_id" => "3463499",
"other_people" => null,
"lab_id" => "UVA",
"protocol_id" => "uva_histag_purification_1.1",
"status" => "success",
"expression_organism" => "E. coli",
"expression_strain" => "BL21 (DE3)-RIPL",
"media_type" => "LB",
"media_volume" => "2000",
"growth_temperature" => "37",
"induction_temperature" => "17",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => null,
"solubility_level" => null,
"inserted" => "2015-03-14 03:00:03.489809+00",
"ins_user_id" => null,
"update" => "2015-03-14 03:00:03.489809+00",
"upd_user_id" => null,
"present_in_lims" => false,
"lims_date" => "2015-03-13",
"dummy" => false,
"Staff" => array(
"id" => "3463499",
"first_name" => "Piotr",
"last_name" => "Sroka",
"email" => "piotr_s@iwonka.med.virginia.edu",
"phone" => "",
"lab_id" => "UVA",
"responsibility" => "",
"databases" => true,
"admin" => false,
"protein_production" => true,
"crystallography" => true,
"pi" => false,
"lab_contact" => false,
"inserted" => "2014-09-11 18:05:18.003554+00",
"updated" => "2014-09-11 18:05:18.003554+00",
"institution_id" => null,
"middle_initials" => null,
"active" => false,
"manager" => false,
"function" => null,
"real_id" => null
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___61789",
"name" => "E .03/09/15",
"data" => array(),
"children" => array()
)
$expression_level = "N/A"
$solubility_level = "N/A"
$spur = array(
"id" => "5719",
"target_id" => "012320",
"purification_suffix" => "917",
"expression_id" => "61789",
"local_expression_id" => "702",
"local_protein_target_id" => "1679",
"local_purification_id" => "917",
"experiment_date_start" => "2015-03-12",
"experiment_date_end" => "2015-03-13",
"staff_id" => "3463499",
"other_people" => null,
"lab_id" => "UVA",
"protocol_id" => "uva_histag_purification_1.1",
"status" => "success",
"description" => "",
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => "",
"final_concentration" => "4.07",
"final_volume" => "0",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2015-03-14 03:00:07.720193+00",
"ins_user_id" => null,
"update" => "2015-03-25 03:00:08.60586+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2015-03-13",
"dummy" => false,
"yield" => null,
"Staff" => array(
"id" => "3463499",
"first_name" => "Piotr",
"last_name" => "Sroka",
"email" => "piotr_s@iwonka.med.virginia.edu",
"phone" => "",
"lab_id" => "UVA",
"responsibility" => "",
"databases" => true,
"admin" => false,
"protein_production" => true,
"crystallography" => true,
"pi" => false,
"lab_contact" => false,
"inserted" => "2014-09-11 18:05:18.003554+00",
"updated" => "2014-09-11 18:05:18.003554+00",
"institution_id" => null,
"middle_initials" => null,
"active" => false,
"manager" => false,
"function" => null,
"real_id" => null
),
"CrystallizationDrop" => array(),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___5719",
"name" => "P .03/12/15"
)
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
