Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "005621"
$split = "___"
$target = array(
"Target" => array(
"id" => "10061",
"target_id" => "005621",
"local_target_id" => "005621",
"locus_tag" => null,
"ncbi_gi" => "19923536",
"ncbi_accession" => "NP_061008.2",
"ncbi_geneid" => "114625",
"ncbi_taxon_id" => "9606",
"gene_name" => "ERMAP",
"common_name" => "erythroid membrane-associated protein precursor [Homo sapiens]",
"ncbi_coded_by_region" => "NM_018538.3:167..1594",
"ncbi_note" => null,
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => " Structural genomics of cell surface anchored Immunoglobulin Superfamily proteins that mediate immune response of T cells; human proteins and their orthologs",
"sequence" => "MEMASSAGSWLSGCLIPLVFLRLSVHVSGHAGDAGKFHVALLGGTAELLCPLSLWPGTVPKEVRWLRSPFPQRSQAVHIFRDGKDQDEDLMPEYKGRTVLVRDAQEGSVTLQILDVRLEDQGSYRCLIQVGNLSKEDTVILQVAAPSVGSLSPSAVALAVILPVLVLLIMVCLCLIWKQRRAKEKLLYEHVTEVDNLLSDHAKEKGKLHKAVKKLRSELKLKRAAANSGWRRARLHFVAVTLDPDTAHPKLILSEDQRCVRLGDRRQPVPDNPQRFDFVVSILGSEYFTTGCHYWEVYVGDKTKWILGVCSESVSRKGKVTASPANGHWLLRQSRGNEYEALTSPQTSFRLKEPPRCVGIFLDYEAGVISFYNVTNKSHIFTFTHNFSGPLRPFFEPCLHDGGKNTAPLVICSELHKSEESIVPRPEGKGHANGDVSLKVNSSLLPPKAPELKDIILSLPPDLGPALQELKAPSF",
"sequence_length" => "475",
"dna_sequence" => "ATGGAGATGGCGAGTTCTGCTGGCTCCTGGCTCTCTGGCTGCCTCATCCCTCTCGTCTTCCTCCGGCTGTCTGTGCATGTGTCAGGCCACGCAGGGGATGCCGGCAAGTTCCACGTGGCCCTACTAGGGGGCACAGCCGAGCTGCTCTGCCCTCTCTCCCTCTGGCCCGGGACGGTACCCAAGGAGGTGAGGTGGCTGCGGTCCCCATTCCCGCAGCGCTCCCAGGCTGTTCACATATTCCGGGATGGGAAGGACCAGGATGAAGATCTGATGCCGGAATATAAGGGGAGGACGGTGCTAGTGAGAGATGCCCAAGAGGGAAGTGTCACTCTGCAGATCCTTGACGTGCGCCTTGAGGACCAAGGGTCTTACCGATGTCTGATCCAAGTTGGAAATCTGAGTAAAGAGGACACCGTGATCCTGCAGGTTGCAGCCCCATCTGTGGGGAGTCTCTCCCCCTCAGCAGTGGCTCTGGCTGTGATCCTGCCTGTCCTGGTACTTCTCATCATGGTGTGCCTTTGCCTTATCTGGAAGCAAAGAAGAGCAAAAGAAAAGCTTCTCTATGAACATGTGACGGAGGTGGACAATCTTCTTTCAGACCATGCTAAAGAAAAAGGAAAACTCCATAAAGCTGTCAAGAAACTCCGGAGTGAACTGAAGTTGAAAAGAGCTGCAGCAAACTCAGGCTGGAGAAGAGCCCGGTTGCATTTTGTGGCAGTGACCCTGGACCCAGACACAGCACATCCCAAACTCATCCTTTCTGAGGACCAAAGATGTGTAAGGCTTGGAGACAGACGGCAGCCTGTACCTGACAACCCCCAGAGATTTGATTTCGTTGTCAGCATCCTAGGCTCTGAGTACTTCACGACTGGCTGCCACTACTGGGAGGTGTATGTGGGAGACAAGACCAAATGGATTCTTGGAGTATGTAGTGAGTCAGTGAGCAGGAAGGGGAAGGTTACTGCCTCACCTGCCAATGGACACTGGCTTCTGCGACAGAGTCGTGGGAATGAGTATGAAGCTCTCACATCCCCGCAGACCTCCTTCCGCCTTAAAGAGCCTCCACGGTGTGTGGGGATTTTCCTGGACTATGAAGCAGGAGTCATCTCTTTCTACAATGTGACCAACAAGTCCCACATCTTTACTTTCACCCACAATTTCTCTGGCCCCCTTCGCCCTTTCTTTGAACCTTGCCTTCATGATGGAGGAAAAAACACAGCACCTCTAGTCATTTGTTCAGAACTACACAAATCAGAGGAATCAATTGTCCCCAGGCCAGAAGGGAAAGGCCATGCTAATGGAGATGTGTCCCTCAAGGTGAACTCTTCTTTACTACCCCCGAAGGCCCCAGAGCTGAAGGATATAATCCTGTCCTTGCCCCCTGACCTTGGCCCAGCCCTTCAGGAGCTCAAGGCTCCTTCTTTTTAG",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "IFN:IgSF (Immune Function Network)",
"selection_phase" => null,
"date_selected" => "2011-01-26",
"date_approved" => "2011-01-26",
"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" => "2011-01-26 21:10:07.802567+00",
"updated" => "2011-01-26 21:10:07.802567+00",
"species_taxon_id" => "9606",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "crystallized",
"hidden" => false,
"submitter_id" => null,
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => null,
"genus_taxon_id" => "9605",
"seguid" => null,
"uniprot_id" => null,
"ec" => null,
"target_family" => null,
"tar_designpool_id" => null,
"community_nominated" => false,
"partnership_nominated" => "IFN",
"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" => "MEMASSAGSWLSGCLIPLVFLRLSVHVSGHAGDAGKFHVALLGGTAELLCPLSLWPGTVPKEVRWLRSPFPQRSQAVHIFRDGKDQDEDLMPEYKGRTVLVRDAQEGSVTLQILDVRLEDQGSYRCLIQVGNLSKEDTVILQVAAPSVGSLSPSAVALAVILPVLVLLIMVCLCLIWKQRRAKEKLLYEHVTEVDNLLSDHAKEKGKLHKAVKKLRSELKLKRAAANSGWRRARLHFVAVTLDPDTAHPKLILSEDQRCVRLGDRRQPVPDNPQRFDFVVSILGSEYFTTGCHYWEVYVGDKTKWILGVCSESVSRKGKVTASPANGHWLLRQSRGNEYEALTSPQTSFRLKEPPRCVGIFLDYEAGVISFYNVTNKSHIFTFTHNFSGPLRPFFEPCLHDGGKNTAPLVICSELHKSEESIVPRPEGKGHANGDVSLKVNSSLLPPKAPELKDIILSLPPDLGPALQELKAPSF",
"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(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array()
)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___005621"
),
array(
"Target___005621",
"ProteinClone___66924"
),
array(
"Target___005621",
"ProteinClone___66924",
"Expression___24336"
),
array(
"Target___005621",
"ProteinClone___63105"
),
array(
"Target___005621",
"ProteinClone___67339"
),
array(
"Target___005621",
"ProteinClone___67339",
"Expression___21525"
),
array(
"Target___005621",
"ProteinClone___67340"
),
array(
"Target___005621",
"ProteinClone___67340",
"Expression___21813"
),
array(
"Target___005621",
"ProteinClone___67340",
"Expression___25169"
)
)
$tips = array(
"Target___005621" => array(
"title" => "Target 005621",
"text" => "erythroid membrane-associated protein precursor [Homo sapiens]"
),
"ProteinClone___66924" => array(
"title" => "Clone",
"text" => "sequence range: 35-154<br>vector: pMAM-Fc<br>person: Mark Stead"
),
"Expression___24336" => array(
"title" => "Expression",
"text" => "expression level: 66.7%<br>solubility level: 0.0%<br>media: Freestyle (1mL)<br>induction: IPTG (37°C)<br>person: Sarah Garrett"
),
"ProteinClone___63105" => array(
"title" => "Clone",
"text" => "sequence range: 88-432<br>vector: pIEX-SEC<br>person: Mark Stead"
),
"ProteinClone___67339" => array(
"title" => "Clone",
"text" => "sequence range: 88-432<br>vector: pMAM-SEC<br>person: Mark Stead"
),
"Expression___21525" => array(
"title" => "Expression",
"text" => "expression level: 33.3%<br>solubility level: 33.3%<br>media: FreeStyle 293 (1mL)<br>induction: IPTG (37°C)<br>person: Rodolfo Chaparro"
),
"ProteinClone___67340" => array(
"title" => "Clone",
"text" => "sequence range: 88-432<br>vector: pDAD-SEC<br>person: Mark Stead"
),
"Expression___21813" => array(
"title" => "Expression",
"text" => "expression level: 33.3%<br>solubility level: 33.3%<br>media: Freestyle 293 (1.5mL)<br>induction: IPTG (37°C)<br>person: Ashok Bandaranayake"
),
"Expression___25169" => array(
"title" => "Expression",
"text" => "expression level: N/A<br>solubility level: N/A<br>media: Freestyle (1000mL)<br>induction: IPTG (37°C)<br>person: Ashok Bandaranayake"
),
"Purification___3702" => array(
"title" => "Purification",
"text" => "final concentration: 0mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Ashok Bandaranayake"
)
)
$root = array(
"id" => "Target___005621",
"name" => "T 005621",
"data" => array()
)
$clones = array(
array(
"id" => "ProteinClone___66924",
"name" => "C .08/08/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___63105",
"name" => "C .01/11/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___67339",
"name" => "C .08/23/12",
"data" => array(),
"children" => array()
)
)
$sclone = array(
"id" => "67340",
"target_id" => "005621",
"clone_suffix" => "24619",
"sequence_start" => "88",
"sequence_end" => "432",
"sequence" => "HAGDAGKFHVALLGGTAELLCPLSLWPGTVPKEVRWLRSPFPQRSQAVHIFRDGKDQDEDLMPEYKGRTVLVRDAQEGSVTLQILDVRLEDQGSYRCLIQVGNLSKEDTVILQVA",
"sequence_comments" => null,
"local_protein_target_id" => "9423",
"local_clone_plate_id" => null,
"local_clone_id" => "24619",
"experiment_date_start" => "2012-08-23",
"experiment_date_end" => "2012-08-23",
"staff_id" => "430",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pDAD-SEC",
"pcr_primer_forward" => "CCTCTCGGCCTGCCTGTGCTAGGCCACGCAGGGGATGCCGG",
"pcr_primer_backward" => "GGTTCTCGCTTCCGCCACCTGCAACCTGCAGGATCACGG",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2012-08-23 17:00:35.967272+00",
"ins_user_id" => null,
"update" => "2014-05-20 02:03:56.418778+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" => "CACGCAGGGGATGCCGGCAAGTTCCACGTGGCCCTACTAGGGGGCACAGCCGAGCTGCTCTGCCCTCTCTCCCTCTGGCCCGGGACGGTACCCAAGGAGGTGAGGTGGCTGCGGTCCCCATTCCCGCAGCGCTCCCAGGCTGTTCACATATTCCGGGATGGGAAGGACCAGGATGAAGATCTGATGCCGGAATATAAGGGGAGGACGGTGCTAGTGAGAGATGCCCAAGAGGGAAGTGTCACTCTGCAGATCCTTGACGTGCGCCTTGAGGACCAAGGGTCTTACCGATGTCTGATCCAAGTTGGAAATCTGAGTAAAGAGGACACCGTGATCCTGCAGGTTGCA",
"lims_date" => "2012-08-23",
"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()
)
)
$iclone = array(
"id" => "ProteinClone___67340",
"name" => "C .08/23/12",
"data" => array(),
"children" => array(
array()
)
)
$sexpr = array(
"id" => "25169",
"target_id" => "005621",
"expression_suffix" => "34630",
"clone_id" => "67340",
"clone_suffix" => "24619",
"local_clone_id" => "24619",
"local_protein_target_id" => "9423",
"local_expression_id" => "34630",
"experiment_date_start" => "2012-10-10",
"experiment_date_end" => "2012-10-17",
"staff_id" => "3143",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Lentivirus Production & Large-Scale Expression",
"status" => "success",
"expression_organism" => "Human",
"expression_strain" => "HEK 293",
"media_type" => "Freestyle",
"media_volume" => "1000",
"growth_temperature" => "37",
"induction_temperature" => "37",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => null,
"solubility_level" => null,
"inserted" => "2012-11-16 19:00:19.562953+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:21:41.452929+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2012-11-16",
"dummy" => false,
"Staff" => array(
"id" => "3143",
"first_name" => "Ashok",
"last_name" => "Bandaranayake",
"email" => "ashok.bandaranayake@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" => "2012-08-27 16:00:01.572026+00",
"updated" => "2012-08-27 16:00:01.572026+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "3143"
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___25169",
"name" => "E .10/10/12",
"data" => array(),
"children" => array()
)
$expression_level = "N/A"
$solubility_level = "N/A"
$spur = array(
"id" => "3702",
"target_id" => "005621",
"purification_suffix" => "4363",
"expression_id" => "25169",
"local_expression_id" => "34630",
"local_protein_target_id" => "9423",
"local_purification_id" => "4363",
"experiment_date_start" => "2012-11-05",
"experiment_date_end" => "2012-11-09",
"staff_id" => "3143",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large-Scale Purification Mammalian Secreted-Fc Fusions",
"status" => "success",
"description" => "",
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => "",
"final_concentration" => "0",
"final_volume" => "0",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2012-11-16 19:00:23.929791+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:29:25.152909+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2012-11-16",
"dummy" => false,
"yield" => null,
"Staff" => array(
"id" => "3143",
"first_name" => "Ashok",
"last_name" => "Bandaranayake",
"email" => "ashok.bandaranayake@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" => "2012-08-27 16:00:01.572026+00",
"updated" => "2012-08-27 16:00:01.572026+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "3143"
),
"CrystallizationDrop" => array(),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___3702",
"name" => "P .11/05/12"
)
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
