Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "006012"
$split = "___"
$target = array(
"Target" => array(
"id" => "10625",
"target_id" => "006012",
"local_target_id" => "006012",
"locus_tag" => null,
"ncbi_gi" => "54036138",
"ncbi_accession" => "Q80W68.1",
"ncbi_geneid" => null,
"ncbi_taxon_id" => "10090",
"gene_name" => "Kirrel",
"common_name" => "RecName: Full=Kin of IRRE-like protein 1; AltName: Full=Kin of irregular chiasm-like protein 1; AltName: Full=Nephrin-like protein 1; Flags: Precursor",
"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" => "MTLESPSTRLMTCQSSLLPEKPRFLSQKMWAPHLVVAYLIFVTLALALPGTQTRFSQEPADQTVVAGQRAVLPCVLLNYSGIVQWTKDGLALGMGQGLKAWPRYRVVGSADAGQYNLEITDAELSDDASYECQATEAALRSRRAKLTVLIPPEETRIDGGPVILLQAGTPYNLTCRAFNAKPAATIIWFRDGTQQEGAVTSTELLKDGKRETTISQLLIEPTDLDIGRVFTCRSMNEAIPNGKETSIELDVHHPPTVTLSIEPQTVLEGERVIFTCQATANPEILGYRWAKGGFLIEDAHESRYETNVDYSFFTEPVSCEVYNKVGSTNVSTLVNVHFAPRIVVYPKPTTTDIGSDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADAGTYTCRAIVPRIGVAEREVPLYVNGPPIISSEAVQFAVRGDGGKVECFIGSTPPPDRIAWAWKENFLEVGTLERYTVERTNSGSGVLSTLTINNVMEADFQTHYNCTAWNSFGPGTAIIQLEEREVLPVGIIAGATIGAGILVVFSFAALVFFLYRRRKGSRKDVTLRKLDIKVETVNREPLTMHSDREDDTASISTATRVMKAIYSSFKDDVDLKQDLRCDTIDTREEYEMKDPTNGYYNVRAHEDRPSSRAVLYADYRAPGPTRFDGRPSSRLSHSSGYAQLNTYSRAPASDYGTEPTPSGPSAPGGTDTTSQLSYENYEKFNSHPFPGAAGYPTYRLGYPQAPPSGLERTPYEAYDPIGKYATATRFSYTSQHSDYGQRFQQRMQTHV",
"sequence_length" => "789",
"dna_sequence" => "ATGACTCTGGAGAGCCCTAGCACACGTCTAATGACCTGCCAATCAAGCCTGCTCCCTGAGAAGCCCAGGTTTCTGAGTCAGAAGATGTGGGCTCCACACTTAGTCGTTGCTTATCTTATCTTTGTGACTTTGGCTTTGGCTTTGCCCGGGACTCAGACTCGCTTCAGCCAGGAGCCAGCTGATCAGACTGTGGTGGCCGGACAGCGGGCGGTGCTCCCGTGTGTGCTCCTTAACTACTCTGGGATTGTACAGTGGACCAAGGACGGGCTGGCCCTGGGTATGGGCCAGGGCCTCAAAGCCTGGCCACGGTACCGGGTCGTGGGCTCTGCGGATGCTGGGCAATACAACTTGGAGATCACAGATGCCGAGCTGTCTGATGACGCTTCCTATGAGTGCCAGGCCACGGAGGCTGCCCTGCGCTCTCGGCGGGCCAAACTCACCGTGCTCATTCCTCCAGAGGAAACAAGGATTGATGGGGGCCCGGTGATTCTGCTGCAAGCAGGCACCCCCTACAACCTCACGTGCAGAGCATTTAATGCCAAACCTGCTGCCACCATCATTTGGTTCCGAGATGGGACACAGCAGGAGGGGGCTGTGACTAGCACGGAGCTGCTGAAGGATGGGAAAAGGGAGACCACAATCAGCCAACTGCTCATTGAGCCCACAGACCTAGACATTGGCCGCGTATTCACCTGTCGCAGTATGAATGAGGCCATCCCCAATGGCAAGGAGACATCCATTGAGCTTGATGTGCACCACCCTCCCACAGTGACTCTGTCCATCGAGCCCCAGACAGTGCTGGAAGGCGAGCGTGTCATTTTTACATGCCAGGCCACAGCCAACCCAGAGATCTTGGGCTACAGGTGGGCCAAAGGGGGCTTCTTGATTGAAGACGCCCATGAGAGTCGCTATGAGACAAACGTTGACTATTCCTTCTTCACGGAGCCTGTGTCTTGTGAGGTTTATAACAAAGTCGGGAGCACCAATGTCAGCACTTTAGTGAATGTTCACTTCGCCCCCCGGATTGTAGTTTACCCAAAGCCCACCACCACAGACATTGGATTTGATGTGACCCTCACCTGTGTCTGGGTTGGGAATCCTCCCCTCACCCTCACCTGGACCAAGAAGGACTCAAACATGGTCCTGAGTAACAGCAATCAACTGTTGCTGAAGTCAGTGACCCAGGCAGATGCTGGCACCTATACCTGCCGGGCCATCGTGCCTCGGATCGGAGTGGCTGAGCGAGAGGTACCGCTTTATGTAAACGGACCTCCTATCATCTCCAGCGAGGCGGTACAGTTTGCTGTGAGAGGTGATGGCGGTGAGGTGGAGTGCTTTATCGGGAGTACCCCACCTCCGGATCGAATTGCATGGGCATGGAAGGAGAACTTCCTCGAGGTGGGGACCCTGGAACGCTACACCGTGGAGAGGACGAACTCAGGCAGCGGTGTGCTGTCCACGCTCACCATTAATAATGTCATGGAGGCGGACTTCCAGACCCACTACAACTGCACTGCCTGGAACAGCTTTGGACCAGGCACAGCCATCATCCAGCTGGAAGAGCGAGAGGTGTTACCTGTGGGCATCATTGCCGGGGCCACCATCGGTGCCGGCATCCTGGTCGTCTTCTCTTTTGCTGCCTTAGTGTTCTTCCTCTACCGACGTCGCAAAGGCAGTCGAAAGGATGTGACGTTGAGGAAGCTGGACATCAAGGTGGAGACGGTGAATCGGGAGCCACTTACGATGCACTCTGACCGGGAGGATGATACTGCCAGCATTTCCACGGCAACGCGGGTCATGAAGGCCATCTACTCGTCCTTTAAGGATGATGTGGATCTGAAGCAGGACCTGCGCTGTGACACCATTGACACCCGGGAAGAGTATGAGATGAAGGATCCCACCAATGGTTATTACAATGTGCGCGCCCACGAAGATCGCCCGTCCTCCAGGGCGGTGCTGTATGCTGACTACCGTGCCCCTGGCCCTACTCGTTTTGATGGGCGCCCGTCATCCCGCCTGTCCCACTCCAGTGGTTATGCCCAGCTCAATACGTACAGCCGGGCCCCTGCCTCTGACTATGGCACAGAGCCTACACCCTCTGGCCCTTCTGCTCCGGGTGGCACCGATACGACCAGCCAGCTGTCCTACGAGAACTATGAGAAGTTCAACTCCCACCCCCTTCCCGGGGCAGCTGGGTATCCTACATACCGTCTAGGCTACCCCCAGGCCCCACCCTCTGGCCTGGAGAGGACCCCCTACGAAGCGTATGACCCTATTGGCAAGTATGCCACCGCCACTCGGTTCTCCTACACCTCTCAGCACTCAGACTATGGCCAGCGATTCCAGCAGCGCATGCAGACTCATGTGTAG",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "IFN:IgSF (Immune Function Network)",
"selection_phase" => null,
"date_selected" => "2011-01-20",
"date_approved" => "2011-02-10",
"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" => "2011-02-10 18:45:43.901606+00",
"updated" => "2011-02-10 18:45:43.901606+00",
"species_taxon_id" => "10090",
"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" => null,
"genus_taxon_id" => "10088",
"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" => "MTLESPSTRLMTCQSSLLPEKPRFLSQKMWAPHLVVAYLIFVTLALALPGTQTRFSQEPADQTVVAGQRAVLPCVLLNYSGIVQWTKDGLALGMGQGLKAWPRYRVVGSADAGQYNLEITDAELSDDASYECQATEAALRSRRAKLTVLIPPEETRIDGGPVILLQAGTPYNLTCRAFNAKPAATIIWFRDGTQQEGAVTSTELLKDGKRETTISQLLIEPTDLDIGRVFTCRSMNEAIPNGKETSIELDVHHPPTVTLSIEPQTVLEGERVIFTCQATANPEILGYRWAKGGFLIEDAHESRYETNVDYSFFTEPVSCEVYNKVGSTNVSTLVNVHFAPRIVVYPKPTTTDIGFDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADAGTYTCRAIVPRIGVAEREVPLYVNGPPIISSEAVQFAVRGDGGEVECFIGSTPPPDRIAWAWKENFLEVGTLERYTVERTNSGSGVLSTLTINNVMEADFQTHYNCTAWNSFGPGTAIIQLEEREVLPVGIIAGATIGAGILVVFSFAALVFFLYRRRKGSRKDVTLRKLDIKVETVNREPLTMHSDREDDTASISTATRVMKAIYSSFKDDVDLKQDLRCDTIDTREEYEMKDPTNGYYNVRAHEDRPSSRAVLYADYRAPGPTRFDGRPSSRLSHSSGYAQLNTYSRAPASDYGTEPTPSGPSAPGGTDTTSQLSYENYEKFNSHPLPGAAGYPTYRLGYPQAPPSGLERTPYEAYDPIGKYATATRFSYTSQHSDYGQRFQQRMQTHV",
"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(),
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array(),
array(),
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)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___006012"
),
array(
"Target___006012",
"ProteinClone___66152"
),
array(
"Target___006012",
"ProteinClone___69462"
),
array(
"Target___006012",
"ProteinClone___69462",
"Expression___26908"
),
array(
"Target___006012",
"ProteinClone___66274"
),
array(
"Target___006012",
"ProteinClone___68646"
),
array(
"Target___006012",
"ProteinClone___68646",
"Expression___22234"
),
array(
"Target___006012",
"ProteinClone___68646",
"Expression___24976"
),
array(
"Target___006012",
"ProteinClone___64662"
),
array(
"Target___006012",
"ProteinClone___64662",
"Expression___24024"
),
array(
"Target___006012",
"ProteinClone___64662",
"Expression___23503"
)
)
$tips = array(
"Target___006012" => array(
"title" => "Target 006012",
"text" => "RecName: Full=Kin of IRRE-like protein 1; AltName: Full=Kin of irregular chiasm-like protein 1; AltName: Full=Nephrin-like protein 1; Flags: Precursor"
),
"ProteinClone___66152" => array(
"title" => "Clone",
"text" => "sequence range: 50-154<br>vector: pPELB30<br>person: Mark Stead"
),
"ProteinClone___69462" => array(
"title" => "Clone",
"text" => "sequence range: 347-427<br>vector: pIEX-sec-C<br>person: Mark Stead"
),
"Expression___26908" => 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___66274" => array(
"title" => "Clone",
"text" => "sequence range: 50-154<br>vector: pSGC-His<br>person: Mark Stead"
),
"ProteinClone___68646" => array(
"title" => "Clone",
"text" => "sequence range: 50-154<br>vector: pSGC-His<br>person: Mark Stead"
),
"Expression___22234" => array(
"title" => "Expression",
"text" => "expression level: 0.0%<br>solubility level: 0.0%<br>media: PASM-52 (0.75mL)<br>induction: IPTG (37°C)<br>person: Ron Seidel"
),
"Expression___24976" => 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___64662" => array(
"title" => "Clone",
"text" => "sequence range: 50-257<br>vector: pIEX-sec-C<br>person: Brandan Hillerich"
),
"Expression___24024" => array(
"title" => "Expression",
"text" => "expression level: 66.7%<br>solubility level: 100.0%<br>media: Express Five SFM (4mL)<br>induction: IPTG (37°C)<br>person: Albe Chan"
),
"Expression___23503" => array(
"title" => "Expression",
"text" => "expression level: 33.3%<br>solubility level: 33.3%<br>media: Express Five SFM (4000mL)<br>induction: IPTG (37°C)<br>person: Scott Garforth"
),
"Purification___3618" => array(
"title" => "Purification",
"text" => "final concentration: 4.9mg/mL<br>SeMet: native<br>affinity tag: na<br>person: Muftah Ahmed"
)
)
$root = array(
"id" => "Target___006012",
"name" => "T 006012",
"data" => array()
)
$clones = array(
array(
"id" => "ProteinClone___66152",
"name" => "C .08/01/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___69462",
"name" => "C .09/20/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___66274",
"name" => "C .08/01/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___68646",
"name" => "C .09/14/12",
"data" => array(),
"children" => array()
)
)
$sclone = array(
"id" => "64662",
"target_id" => "006012",
"clone_suffix" => "21005",
"sequence_start" => "50",
"sequence_end" => "257",
"sequence" => "GTQTRFSQEPADQTVVAGQRAVLPCVLLNYSGIVQWTKDGLALGMGQGLKAWPRYRVVGSADAGQYNLEITDAELSDDASYECQATEAALRSRRAKLTVLIPPEETRIDGGPVILLQAGTPYNLTCRAFNAKPAATIIWFRDGTQQEGAVTSTELLKDGKRETTISQLLIEPTDLDIGRVFTCRSMNEAIPNGKETSIELDVHHPPTV",
"sequence_comments" => null,
"local_protein_target_id" => "10299",
"local_clone_plate_id" => null,
"local_clone_id" => "21005",
"experiment_date_start" => "2012-07-02",
"experiment_date_end" => "2012-07-02",
"staff_id" => "23",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pIEX-sec-C",
"pcr_primer_forward" => "AGGATTATGGAGGCGGGACTCAGACTCGCTTCAG",
"pcr_primer_backward" => "GATTGGAAGTAGAGGTTCTCTGCCACTGTGGGAGGGTGGTGC",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2012-07-02 19:00:18.333285+00",
"ins_user_id" => null,
"update" => "2014-05-20 02:03:24.425223+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" => "GGGACTCAGACTCGCTTCAGCCAGGAGCCAGCTGATCAGACTGTGGTGGCCGGACAGCGGGCGGTGCTCCCGTGTGTGCTCCTTAACTACTCTGGGATTGTACAGTGGACCAAGGACGGGCTGGCCCTGGGTATGGGCCAGGGCCTCAAAGCCTGGCCACGGTACCGGGTCGTGGGCTCTGCGGATGCTGGGCAATACAACTTGGAGATCACAGATGCCGAGCTGTCTGATGACGCTTCCTATGAGTGCCAGGCCACGGAGGCTGCCCTGCGCTCTCGGCGGGCCAAACTCACCGTGCTCATTCCTCCAGAGGAAACAAGGATTGATGGGGGCCCGGTGATTCTGCTGCAAGCAGGCACCCCCTACAACCTCACGTGCAGAGCATTTAATGCCAAACCTGCTGCCACCATCATTTGGTTCCGAGATGGGACACAGCAGGAGGGGGCTGTGACTAGCACGGAGCTGCTGAAGGATGGGAAAAGGGAGACCACAATCAGCCAACTGCTCATTGAGCCCACAGACCTAGACATTGGCCGCGTATTCACCTGTCGCAGTATGAATGAGGCCATCCCCAATGGCAAGGAGACATCCATTGAGCTTGATGTGCACCACCCTCCCACAGTG",
"lims_date" => "2012-07-02",
"dummy" => false,
"type" => null,
"clone_annotation" => null,
"optimized_dna_sequence" => null,
"optimized" => false,
"truncated" => false,
"synthetic" => false,
"Staff" => array(
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"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,
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"real_id" => "23"
),
"Expression" => array(
array(),
array()
)
)
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"id" => "ProteinClone___64662",
"name" => "C .07/02/12",
"data" => array(),
"children" => array(
array()
)
)
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"id" => "23503",
"target_id" => "006012",
"expression_suffix" => "32565",
"clone_id" => "64662",
"clone_suffix" => "21005",
"local_clone_id" => "21005",
"local_protein_target_id" => "10299",
"local_expression_id" => "32565",
"experiment_date_start" => "2012-10-09",
"experiment_date_end" => "2012-10-09",
"staff_id" => "355",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large scale insect expression- secreted plus kifunensine",
"status" => "success",
"expression_organism" => "Insect",
"expression_strain" => "Hi5",
"media_type" => "Express Five SFM",
"media_volume" => "4000",
"growth_temperature" => "37",
"induction_temperature" => "37",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => "33.3333",
"solubility_level" => "33.3333",
"inserted" => "2012-10-12 21:00:22.30748+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:21:05.43455+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2012-10-12",
"dummy" => false,
"Staff" => array(
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"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___23503",
"name" => "E .10/09/12",
"data" => array(),
"children" => array()
)
$expression_level = "33.3%"
$solubility_level = "33.3%"
$spur = array(
"id" => "3618",
"target_id" => "006012",
"purification_suffix" => "4213",
"expression_id" => "23503",
"local_expression_id" => "32565",
"local_protein_target_id" => "10299",
"local_purification_id" => "4213",
"experiment_date_start" => "2012-10-15",
"experiment_date_end" => "2012-10-16",
"staff_id" => "1825",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large-Scale Automated Protein Purification",
"status" => "success",
"description" => null,
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => null,
"final_concentration" => "4.9",
"final_volume" => "8500",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2012-10-17 16:00:42.284609+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:29:23.192376+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2012-10-17",
"dummy" => false,
"yield" => null,
"Staff" => array(
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"first_name" => "Muftah",
"last_name" => "Ahmed",
"email" => "muftah.ahmed@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2012-06-22 21:00:37.397023+00",
"updated" => "2012-06-22 21:00:37.397023+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
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"function" => null,
"real_id" => "1825"
),
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$ipur = array(
"id" => "Purification___3618",
"name" => "P .10/15/12"
)
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
