Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "012730"
$split = "___"
$target = array(
"Target" => array(
"id" => "13151",
"target_id" => "012730",
"local_target_id" => "012730",
"locus_tag" => null,
"ncbi_gi" => null,
"ncbi_accession" => null,
"ncbi_geneid" => null,
"ncbi_taxon_id" => "9813",
"gene_name" => null,
"common_name" => "inducible T-cell co-stimulator ",
"ncbi_coded_by_region" => null,
"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" => "MKSVIWYFFLFCFQVDVLTGERNDSTKPEMCEFHKGGIQITCKHNETIQQYKMRLLKGGQVLCELTKTNESTNTVCSIKNLEFCQLSNNSISFFLYNLNTYHASDYFCRLVIFDPPPYRVQNLSGEYLHVYESELCCQLKFWLPIICAAFLVLYILGCIAVCWLTKKKYQSTVHDTNSEYMSMAAVNTAKMPGPRDAMF",
"sequence_length" => "199",
"dna_sequence" => "ATGAAGTCAGTCATCTGGTATTTCTTTCTCTTCTGCTTCCAAGTTGATGTTCTAACAGGAGAAAGAAATGATTCTACGAAGCCTGAGATGTGTGAATTTCACAAGGGAGGCATACAAATTACGTGCAAACACAATGAGACAATCCAGCAGTATAAAATGAGGCTGCTGAAAGGGGGCCAAGTACTGTGTGAGCTCACCAAAACCAACGAAAGCACAAACACAGTGTGCAGCATCAAGAATCTGGAGTTCTGTCAGCTGTCCAATAACAGCATCTCATTTTTTCTGTATAATTTGAACACCTACCATGCCAGTGACTACTTTTGCCGACTCGTCATTTTTGATCCTCCTCCTTATCGTGTACAGAATCTTAGTGGAGAATATCTGCATGTTTATGAATCAGAGCTTTGCTGCCAGCTGAAGTTCTGGTTGCCCATCATCTGTGCGGCTTTTCTTGTACTCTACATACTTGGGTGTATAGCTGTCTGTTGGCTTACAAAAAAGAAGTATCAGTCCACGGTGCATGACACTAACAGTGAGTACATGTCCATGGCAGCAGTGAACACAGCGAAAATGCCCGGACCCAGAGATGCAATGTTC",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "IFN:IgSF (Immune Function Network)",
"selection_phase" => null,
"date_selected" => "2011-09-08",
"date_approved" => "2011-09-08",
"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" => "2011-09-16 16:43:44.477855+00",
"updated" => "2011-09-16 16:43:44.477855+00",
"species_taxon_id" => "9813",
"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" => "PSI:IFN:IGSF batch 1",
"genus_taxon_id" => "9812",
"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" => null,
"family_coverage" => null,
"family_coverage_date" => null,
"distribution_lab" => null,
"uniprot_accession" => null,
"protocol_id" => "Target_selection",
"ensembl_protein_id" => "ENSPCAP00000012061",
"ensembl_gene_id" => "ENSPCAG00000012941",
"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(),
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___012730"
),
array(
"Target___012730",
"ProteinClone___182244"
),
array(
"Target___012730",
"ProteinClone___77083"
),
array(
"Target___012730",
"ProteinClone___77083",
"Expression___32842"
),
array(
"Target___012730",
"ProteinClone___72779"
),
array(
"Target___012730",
"ProteinClone___72779",
"Expression___31182"
),
array(
"Target___012730",
"ProteinClone___193680"
),
array(
"Target___012730",
"ProteinClone___193678"
),
array(
"Target___012730",
"ProteinClone___193670"
),
array(
"Target___012730",
"ProteinClone___70094"
),
array(
"Target___012730",
"ProteinClone___70094",
"Expression___23586"
),
array(
"Target___012730",
"ProteinClone___183531"
),
array(
"Target___012730",
"ProteinClone___183525"
),
array(
"Target___012730",
"ProteinClone___183527"
),
array(
"Target___012730",
"ProteinClone___183522"
),
array(
"Target___012730",
"ProteinClone___183523"
),
array(
"Target___012730",
"ProteinClone___183524"
),
array(
"Target___012730",
"ProteinClone___183526"
),
array(
"Target___012730",
"ProteinClone___183528"
),
array(
"Target___012730",
"ProteinClone___183529"
),
array(
"Target___012730",
"ProteinClone___183530"
),
array(
"Target___012730",
"ProteinClone___183530",
"Expression___60059"
),
array(
"Target___012730",
"ProteinClone___183530",
"Expression___60160"
)
)
$tips = array(
"Target___012730" => array(
"title" => "Target 012730",
"text" => "inducible T-cell co-stimulator "
),
"ProteinClone___182244" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pNYCOMPSC<br>person: Brandan Hillerich"
),
"ProteinClone___77083" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pNYCOMPSC<br>person: Mark Stead"
),
"Expression___32842" => array(
"title" => "Expression",
"text" => "expression level: 33.3%<br>solubility level: 0.0%<br>media: PSAM-5052 (0.75mL)<br>induction: IPTG (37°C)<br>person: Mark Stead"
),
"ProteinClone___72779" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Mark Stead"
),
"Expression___31182" => array(
"title" => "Expression",
"text" => "expression level: 0.0%<br>solubility level: 0.0%<br>media: Express Five SFM (4mL)<br>induction: IPTG (37°C)<br>person: Albe Chan"
),
"ProteinClone___193680" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pNYCOMPSC<br>person: Mark Stead"
),
"ProteinClone___193678" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pNYCOMPSC<br>person: Mark Stead"
),
"ProteinClone___193670" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pNYCOMPSC<br>person: Mark Stead"
),
"ProteinClone___70094" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pAVITAG-Tagless<br>person: Mark Stead"
),
"Expression___23586" => array(
"title" => "Expression",
"text" => "expression level: 0.0%<br>solubility level: 0.0%<br>media: PASM-5052 (0.75mL)<br>induction: IPTG (37°C)<br>person: Sukanya Chowdhury"
),
"ProteinClone___183531" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183525" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183527" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183522" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183523" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183524" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183526" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183528" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183529" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"ProteinClone___183530" => array(
"title" => "Clone",
"text" => "sequence range: 0-0<br>vector: pIEX-sec-C<br>person: Swetha Chamala"
),
"Expression___60059" => array(
"title" => "Expression",
"text" => "expression level: 0.0%<br>solubility level: 0.0%<br>media: Express Five SFM (3000mL)<br>induction: IPTG (37°C)<br>person: Scott Garforth"
),
"Expression___60160" => array(
"title" => "Expression",
"text" => "expression level: 33.3%<br>solubility level: 33.3%<br>media: Express Five SFM (3000mL)<br>induction: IPTG (37°C)<br>person: Scott Garforth"
),
"Purification___5446" => array(
"title" => "Purification",
"text" => "final concentration: 0mg/mL<br>SeMet: native<br>affinity tag: na<br>person: John Attonito"
)
)
$root = array(
"id" => "Target___012730",
"name" => "T 012730",
"data" => array()
)
$clones = array(
array(
"id" => "ProteinClone___182244",
"name" => "C .08/14/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___77083",
"name" => "C .03/25/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___72779",
"name" => "C .12/05/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___193680",
"name" => "C .09/10/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___193678",
"name" => "C .09/10/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___193670",
"name" => "C .09/10/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___70094",
"name" => "C .10/10/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183531",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183525",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183527",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183522",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183523",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183524",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183526",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183528",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___183529",
"name" => "C .08/28/13",
"data" => array(),
"children" => array()
)
)
$sclone = array(
"id" => "183530",
"target_id" => "012730",
"clone_suffix" => "46359",
"sequence_start" => "0",
"sequence_end" => "0",
"sequence" => "ERNDSTKPEMCEFHKGGIQITCKHNETIQQYKMRLLKGGQVLCELTKTNESTNTVCSIKNLEFCQLSNNSISFFLYNLNTYHASDYFCRLVIFDPPPYRVQNLS",
"sequence_comments" => null,
"local_protein_target_id" => "13733",
"local_clone_plate_id" => null,
"local_clone_id" => "46359",
"experiment_date_start" => "2013-08-28",
"experiment_date_end" => "2013-08-28",
"staff_id" => "450083",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pIEX-sec-C",
"pcr_primer_forward" => "AGGATTATGGAGGCGAGAGAAACGATTCCACTAAGCC",
"pcr_primer_backward" => "GATTGGAAGTAGAGGTTCTCTGCCGAGAGGTTCTGGACGCGG",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-08-28 14:00:16.355816+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:11:36.878877+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" => "GAGAGAAACGATTCCACTAAGCCAGAAATGTGCGAGTTCCACAAGGGCGGCATCCAGATCACCTGTAAGCACAACGAAACCATCCAGCAGTACAAGATGCGTCTGCTCAAGGGTGGCCAAGTTTTGTGCGAGCTGACCAAGACTAACGAAAGCACAAACACCGTGTGCTCAATCAAGAACTTGGAGTTCTGTCAGCTGTCTAACAACTCCATCTCTTTCTTCCTCTACAACTTGAACACTTACCACGCTTCAGACTACTTCTGTCGTCTGGTCATCTTCGATCCCCCTCCCTACCGCGTCCAGAACCTCTCG",
"lims_date" => "2013-08-28",
"dummy" => false,
"type" => null,
"clone_annotation" => null,
"optimized_dna_sequence" => null,
"optimized" => false,
"truncated" => false,
"synthetic" => false,
"Staff" => array(
"id" => "450083",
"first_name" => "Swetha",
"last_name" => "Chamala",
"email" => "swetha.chamala@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" => "2013-07-24 01:00:02.239224+00",
"updated" => "2013-07-24 01:00:02.239224+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "450083"
),
"Expression" => array(
array(),
array(),
array(),
array(),
array()
)
)
$iclone = array(
"id" => "ProteinClone___183530",
"name" => "C .08/28/13",
"data" => array(),
"children" => array(
array()
)
)
$sexpr = array(
"id" => "60160",
"target_id" => "012730",
"expression_suffix" => "56461",
"clone_id" => "183530",
"clone_suffix" => "46359",
"local_clone_id" => "46359",
"local_protein_target_id" => "13733",
"local_expression_id" => "56461",
"experiment_date_start" => "2013-12-06",
"experiment_date_end" => "2013-12-10",
"staff_id" => "355",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large scale insect expression- secreted",
"status" => "success",
"expression_organism" => "Insect",
"expression_strain" => "High Five",
"media_type" => "Express Five SFM",
"media_volume" => "3000",
"growth_temperature" => "37",
"induction_temperature" => "37",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => "33.3333",
"solubility_level" => "33.3333",
"inserted" => "2013-12-17 15:00:39.990113+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:27:21.193642+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-12-17",
"dummy" => false,
"Staff" => array(
"id" => "355",
"first_name" => "Scott",
"last_name" => "Garforth",
"email" => "scott.garforth@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" => "2011-03-22 14:36:38.247355+00",
"updated" => "2011-03-22 14:36:38.247355+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "355"
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___60160",
"name" => "E .12/06/13",
"data" => array(),
"children" => array()
)
$expression_level = "33.3%"
$solubility_level = "33.3%"
$spur = array(
"id" => "5446",
"target_id" => "012730",
"purification_suffix" => "6820",
"expression_id" => "60160",
"local_expression_id" => "56461",
"local_protein_target_id" => "13733",
"local_purification_id" => "6820",
"experiment_date_start" => "2013-12-16",
"experiment_date_end" => "2013-12-17",
"staff_id" => "450145",
"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",
"final_volume" => "0",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-12-19 03:11:53.245271+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:29:53.746258+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-12-18",
"dummy" => false,
"yield" => null,
"Staff" => array(
"id" => "450145",
"first_name" => "John",
"last_name" => "Attonito",
"email" => "john.attonito@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" => "2013-08-23 01:00:02.115165+00",
"updated" => "2013-08-23 01:00:02.115165+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "450145"
),
"CrystallizationDrop" => array(),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___5446",
"name" => "P .12/16/13"
)
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