CA2399272A1 - Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques: in silico cell - Google Patents
Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques: in silico cell Download PDFInfo
- Publication number
- CA2399272A1 CA2399272A1 CA002399272A CA2399272A CA2399272A1 CA 2399272 A1 CA2399272 A1 CA 2399272A1 CA 002399272 A CA002399272 A CA 002399272A CA 2399272 A CA2399272 A CA 2399272A CA 2399272 A1 CA2399272 A1 CA 2399272A1
- Authority
- CA
- Canada
- Prior art keywords
- biological
- model
- recited
- generate
- data structures
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 238000000034 method Methods 0.000 title claims abstract description 67
- 230000002068 genetic effect Effects 0.000 title abstract description 25
- 238000000126 in silico method Methods 0.000 title description 2
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 97
- 230000008569 process Effects 0.000 claims abstract description 42
- 210000000056 organ Anatomy 0.000 claims abstract description 41
- 230000001413 cellular effect Effects 0.000 claims abstract description 30
- 230000037361 pathway Effects 0.000 claims abstract description 23
- 230000031018 biological processes and functions Effects 0.000 claims abstract description 22
- 102000004169 proteins and genes Human genes 0.000 claims description 37
- 230000006870 function Effects 0.000 claims description 34
- 230000002452 interceptive effect Effects 0.000 claims description 23
- 230000003915 cell function Effects 0.000 claims description 13
- 230000007704 transition Effects 0.000 claims description 12
- 230000033077 cellular process Effects 0.000 claims description 10
- 238000004422 calculation algorithm Methods 0.000 claims description 9
- 238000010586 diagram Methods 0.000 claims description 8
- 239000000203 mixture Substances 0.000 claims description 7
- 230000004791 biological behavior Effects 0.000 claims description 5
- 238000009509 drug development Methods 0.000 claims description 3
- 238000009533 lab test Methods 0.000 claims 1
- 238000005094 computer simulation Methods 0.000 abstract description 19
- 230000001225 therapeutic effect Effects 0.000 abstract description 7
- 230000008846 dynamic interplay Effects 0.000 abstract description 3
- 238000005312 nonlinear dynamic Methods 0.000 abstract description 3
- 238000007877 drug screening Methods 0.000 abstract description 2
- 239000002547 new drug Substances 0.000 abstract description 2
- 210000004027 cell Anatomy 0.000 description 110
- 238000006243 chemical reaction Methods 0.000 description 31
- 210000001519 tissue Anatomy 0.000 description 29
- 230000006399 behavior Effects 0.000 description 19
- 210000001744 T-lymphocyte Anatomy 0.000 description 17
- 230000000694 effects Effects 0.000 description 16
- LCTONWCANYUPML-UHFFFAOYSA-M Pyruvate Chemical compound CC(=O)C([O-])=O LCTONWCANYUPML-UHFFFAOYSA-M 0.000 description 15
- 238000004088 simulation Methods 0.000 description 13
- 238000005842 biochemical reaction Methods 0.000 description 12
- 230000014509 gene expression Effects 0.000 description 11
- 201000010099 disease Diseases 0.000 description 10
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 10
- 239000000543 intermediate Substances 0.000 description 9
- 230000003834 intracellular effect Effects 0.000 description 9
- 108090000978 Interleukin-4 Proteins 0.000 description 8
- 230000004069 differentiation Effects 0.000 description 8
- 239000002207 metabolite Substances 0.000 description 8
- 101710088194 Dehydrogenase Proteins 0.000 description 7
- 230000009471 action Effects 0.000 description 7
- 230000008859 change Effects 0.000 description 7
- 210000003463 organelle Anatomy 0.000 description 7
- ZSLZBFCDCINBPY-ZSJPKINUSA-N acetyl-CoA Chemical compound O[C@@H]1[C@H](OP(O)(O)=O)[C@@H](COP(O)(=O)OP(O)(=O)OCC(C)(C)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C)O[C@H]1N1C2=NC=NC(N)=C2N=C1 ZSLZBFCDCINBPY-ZSJPKINUSA-N 0.000 description 6
- 230000015572 biosynthetic process Effects 0.000 description 6
- 239000011575 calcium Substances 0.000 description 6
- 206010039073 rheumatoid arthritis Diseases 0.000 description 6
- 230000000007 visual effect Effects 0.000 description 6
- 108090000695 Cytokines Proteins 0.000 description 5
- 102000004127 Cytokines Human genes 0.000 description 5
- 101000819111 Homo sapiens Trans-acting T-cell-specific transcription factor GATA-3 Proteins 0.000 description 5
- 108090000862 Ion Channels Proteins 0.000 description 5
- 102000004310 Ion Channels Human genes 0.000 description 5
- 102100021386 Trans-acting T-cell-specific transcription factor GATA-3 Human genes 0.000 description 5
- 230000004913 activation Effects 0.000 description 5
- 238000004458 analytical method Methods 0.000 description 5
- 229940079593 drug Drugs 0.000 description 5
- 239000003814 drug Substances 0.000 description 5
- 230000005764 inhibitory process Effects 0.000 description 5
- 230000010354 integration Effects 0.000 description 5
- 239000012528 membrane Substances 0.000 description 5
- 230000019491 signal transduction Effects 0.000 description 5
- 230000011664 signaling Effects 0.000 description 5
- 241000894007 species Species 0.000 description 5
- ZKHQWZAMYRWXGA-KQYNXXCUSA-J ATP(4-) Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@@H]1O[C@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O ZKHQWZAMYRWXGA-KQYNXXCUSA-J 0.000 description 4
- ZKHQWZAMYRWXGA-UHFFFAOYSA-N Adenosine triphosphate Natural products C1=NC=2C(N)=NC=NC=2N1C1OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C1O ZKHQWZAMYRWXGA-UHFFFAOYSA-N 0.000 description 4
- 206010061818 Disease progression Diseases 0.000 description 4
- 102000004190 Enzymes Human genes 0.000 description 4
- 108090000790 Enzymes Proteins 0.000 description 4
- 101000914514 Homo sapiens T-cell-specific surface glycoprotein CD28 Proteins 0.000 description 4
- 101150037263 PIP2 gene Proteins 0.000 description 4
- 101150057388 Reln gene Proteins 0.000 description 4
- 101100262439 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) UBA2 gene Proteins 0.000 description 4
- 102100036011 T-cell surface glycoprotein CD4 Human genes 0.000 description 4
- 102100027213 T-cell-specific surface glycoprotein CD28 Human genes 0.000 description 4
- 210000003719 b-lymphocyte Anatomy 0.000 description 4
- 230000008276 biophysical mechanism Effects 0.000 description 4
- 238000007357 dehydrogenase reaction Methods 0.000 description 4
- 230000018109 developmental process Effects 0.000 description 4
- 230000005750 disease progression Effects 0.000 description 4
- 230000004907 flux Effects 0.000 description 4
- 230000003993 interaction Effects 0.000 description 4
- 210000002540 macrophage Anatomy 0.000 description 4
- 230000035790 physiological processes and functions Effects 0.000 description 4
- 230000004044 response Effects 0.000 description 4
- 238000003786 synthesis reaction Methods 0.000 description 4
- 238000002560 therapeutic procedure Methods 0.000 description 4
- 240000005020 Acaciella glauca Species 0.000 description 3
- 102100034798 CCAAT/enhancer-binding protein beta Human genes 0.000 description 3
- OYPRJOBELJOOCE-UHFFFAOYSA-N Calcium Chemical compound [Ca] OYPRJOBELJOOCE-UHFFFAOYSA-N 0.000 description 3
- 108091006146 Channels Proteins 0.000 description 3
- 101000945963 Homo sapiens CCAAT/enhancer-binding protein beta Proteins 0.000 description 3
- 101001033312 Homo sapiens Interleukin-4 receptor subunit alpha Proteins 0.000 description 3
- 101000599048 Homo sapiens Interleukin-6 receptor subunit alpha Proteins 0.000 description 3
- 102100039078 Interleukin-4 receptor subunit alpha Human genes 0.000 description 3
- 102100037792 Interleukin-6 receptor subunit alpha Human genes 0.000 description 3
- 102100034404 Nuclear factor of activated T-cells, cytoplasmic 1 Human genes 0.000 description 3
- 101710151542 Nuclear factor of activated T-cells, cytoplasmic 1 Proteins 0.000 description 3
- 108091000080 Phosphotransferase Proteins 0.000 description 3
- 102000005886 STAT4 Transcription Factor Human genes 0.000 description 3
- 108010019992 STAT4 Transcription Factor Proteins 0.000 description 3
- 238000013459 approach Methods 0.000 description 3
- 208000006673 asthma Diseases 0.000 description 3
- 230000008901 benefit Effects 0.000 description 3
- 230000008238 biochemical pathway Effects 0.000 description 3
- 230000003851 biochemical process Effects 0.000 description 3
- 210000004556 brain Anatomy 0.000 description 3
- 229910052791 calcium Inorganic materials 0.000 description 3
- 238000010276 construction Methods 0.000 description 3
- 238000011161 development Methods 0.000 description 3
- 238000005516 engineering process Methods 0.000 description 3
- 230000036541 health Effects 0.000 description 3
- 150000002500 ions Chemical class 0.000 description 3
- 238000013178 mathematical model Methods 0.000 description 3
- 210000004789 organ system Anatomy 0.000 description 3
- 102000020233 phosphotransferase Human genes 0.000 description 3
- 235000003499 redwood Nutrition 0.000 description 3
- 230000001105 regulatory effect Effects 0.000 description 3
- 230000032258 transport Effects 0.000 description 3
- 108010029697 CD40 Ligand Proteins 0.000 description 2
- 102100032937 CD40 ligand Human genes 0.000 description 2
- 102000004163 DNA-directed RNA polymerases Human genes 0.000 description 2
- 108090000626 DNA-directed RNA polymerases Proteins 0.000 description 2
- 108090000176 Interleukin-13 Proteins 0.000 description 2
- 102000003816 Interleukin-13 Human genes 0.000 description 2
- 102000004257 Potassium Channel Human genes 0.000 description 2
- 210000004241 Th2 cell Anatomy 0.000 description 2
- 239000012190 activator Substances 0.000 description 2
- 230000003044 adaptive effect Effects 0.000 description 2
- 239000000427 antigen Substances 0.000 description 2
- 102000036639 antigens Human genes 0.000 description 2
- 108091007433 antigens Proteins 0.000 description 2
- 238000004364 calculation method Methods 0.000 description 2
- 230000000747 cardiac effect Effects 0.000 description 2
- 210000000170 cell membrane Anatomy 0.000 description 2
- 210000003850 cellular structure Anatomy 0.000 description 2
- 239000013626 chemical specie Substances 0.000 description 2
- 238000010205 computational analysis Methods 0.000 description 2
- 239000000470 constituent Substances 0.000 description 2
- 238000005314 correlation function Methods 0.000 description 2
- 210000000172 cytosol Anatomy 0.000 description 2
- 230000034994 death Effects 0.000 description 2
- 238000007876 drug discovery Methods 0.000 description 2
- 238000009472 formulation Methods 0.000 description 2
- 239000003446 ligand Substances 0.000 description 2
- 239000000463 material Substances 0.000 description 2
- 239000011159 matrix material Substances 0.000 description 2
- 230000004060 metabolic process Effects 0.000 description 2
- 150000007523 nucleic acids Chemical group 0.000 description 2
- 230000008520 organization Effects 0.000 description 2
- 230000000704 physical effect Effects 0.000 description 2
- 108020001213 potassium channel Proteins 0.000 description 2
- 238000004445 quantitative analysis Methods 0.000 description 2
- 239000000376 reactant Substances 0.000 description 2
- 230000007115 recruitment Effects 0.000 description 2
- 230000002441 reversible effect Effects 0.000 description 2
- 238000012163 sequencing technique Methods 0.000 description 2
- 239000000126 substance Substances 0.000 description 2
- 230000026676 system process Effects 0.000 description 2
- 238000013334 tissue model Methods 0.000 description 2
- PRPINYUDVPFIRX-UHFFFAOYSA-N 1-naphthaleneacetic acid Chemical compound C1=CC=C2C(CC(=O)O)=CC=CC2=C1 PRPINYUDVPFIRX-UHFFFAOYSA-N 0.000 description 1
- 241000208140 Acer Species 0.000 description 1
- 206010001497 Agitation Diseases 0.000 description 1
- 241000219194 Arabidopsis Species 0.000 description 1
- 108010041397 CD4 Antigens Proteins 0.000 description 1
- 101150013553 CD40 gene Proteins 0.000 description 1
- 102000004631 Calcineurin Human genes 0.000 description 1
- 108010042955 Calcineurin Proteins 0.000 description 1
- 101001059930 Drosophila melanogaster Transcription factor kayak, isoforms A/B/F Proteins 0.000 description 1
- 101001059931 Drosophila melanogaster Transcription factor kayak, isoforms D/sro Proteins 0.000 description 1
- 241000588724 Escherichia coli Species 0.000 description 1
- 108010003338 GATA3 Transcription Factor Proteins 0.000 description 1
- 102000004610 GATA3 Transcription Factor Human genes 0.000 description 1
- 101001066288 Gallus gallus GATA-binding factor 3 Proteins 0.000 description 1
- 101150106931 IFNG gene Proteins 0.000 description 1
- 101150015560 IL5 gene Proteins 0.000 description 1
- 206010061218 Inflammation Diseases 0.000 description 1
- 108010002352 Interleukin-1 Proteins 0.000 description 1
- 108010002616 Interleukin-5 Proteins 0.000 description 1
- 108090001005 Interleukin-6 Proteins 0.000 description 1
- 101150069380 JAK3 gene Proteins 0.000 description 1
- 108090000301 Membrane transport proteins Proteins 0.000 description 1
- 102000003939 Membrane transport proteins Human genes 0.000 description 1
- 108091028043 Nucleic acid sequence Proteins 0.000 description 1
- 102000038030 PI3Ks Human genes 0.000 description 1
- 108091007960 PI3Ks Proteins 0.000 description 1
- 230000010799 Receptor Interactions Effects 0.000 description 1
- 229930001406 Ryanodine Natural products 0.000 description 1
- 238000012300 Sequence Analysis Methods 0.000 description 1
- 206010041235 Snoring Diseases 0.000 description 1
- 230000006044 T cell activation Effects 0.000 description 1
- 108091008874 T cell receptors Proteins 0.000 description 1
- 102000016266 T-Cell Antigen Receptors Human genes 0.000 description 1
- 108091023040 Transcription factor Proteins 0.000 description 1
- 102000040945 Transcription factor Human genes 0.000 description 1
- 108060008682 Tumor Necrosis Factor Proteins 0.000 description 1
- 102100040247 Tumor necrosis factor Human genes 0.000 description 1
- 102100040245 Tumor necrosis factor receptor superfamily member 5 Human genes 0.000 description 1
- 230000005856 abnormality Effects 0.000 description 1
- 238000009825 accumulation Methods 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 238000010171 animal model Methods 0.000 description 1
- 230000002917 arthritic effect Effects 0.000 description 1
- 206010003246 arthritis Diseases 0.000 description 1
- 210000003651 basophil Anatomy 0.000 description 1
- 230000033228 biological regulation Effects 0.000 description 1
- 230000003185 calcium uptake Effects 0.000 description 1
- 210000004413 cardiac myocyte Anatomy 0.000 description 1
- 230000003197 catalytic effect Effects 0.000 description 1
- 230000022131 cell cycle Effects 0.000 description 1
- 230000024245 cell differentiation Effects 0.000 description 1
- 230000010261 cell growth Effects 0.000 description 1
- 230000003822 cell turnover Effects 0.000 description 1
- 230000019522 cellular metabolic process Effects 0.000 description 1
- 230000036755 cellular response Effects 0.000 description 1
- 230000005754 cellular signaling Effects 0.000 description 1
- 239000007806 chemical reaction intermediate Substances 0.000 description 1
- 239000003153 chemical reaction reagent Substances 0.000 description 1
- 238000003759 clinical diagnosis Methods 0.000 description 1
- 150000001875 compounds Chemical class 0.000 description 1
- 230000002153 concerted effect Effects 0.000 description 1
- 230000001276 controlling effect Effects 0.000 description 1
- 238000007796 conventional method Methods 0.000 description 1
- 230000008878 coupling Effects 0.000 description 1
- 238000010168 coupling process Methods 0.000 description 1
- 238000005859 coupling reaction Methods 0.000 description 1
- 230000016396 cytokine production Effects 0.000 description 1
- 210000000805 cytoplasm Anatomy 0.000 description 1
- 238000007405 data analysis Methods 0.000 description 1
- 238000013500 data storage Methods 0.000 description 1
- 230000001934 delay Effects 0.000 description 1
- 210000004443 dendritic cell Anatomy 0.000 description 1
- 238000004141 dimensional analysis Methods 0.000 description 1
- 230000000857 drug effect Effects 0.000 description 1
- 239000003596 drug target Substances 0.000 description 1
- 238000000635 electron micrograph Methods 0.000 description 1
- 238000006911 enzymatic reaction Methods 0.000 description 1
- 239000002532 enzyme inhibitor Substances 0.000 description 1
- 229940125532 enzyme inhibitor Drugs 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 238000004880 explosion Methods 0.000 description 1
- 238000011223 gene expression profiling Methods 0.000 description 1
- 230000002414 glycolytic effect Effects 0.000 description 1
- 230000013595 glycosylation Effects 0.000 description 1
- 238000006206 glycosylation reaction Methods 0.000 description 1
- 210000002266 hair cells auditory Anatomy 0.000 description 1
- 210000003630 histaminocyte Anatomy 0.000 description 1
- 210000002865 immune cell Anatomy 0.000 description 1
- 210000000987 immune system Anatomy 0.000 description 1
- 230000006872 improvement Effects 0.000 description 1
- 238000010348 incorporation Methods 0.000 description 1
- 239000012678 infectious agent Substances 0.000 description 1
- 208000015181 infectious disease Diseases 0.000 description 1
- 208000027866 inflammatory disease Diseases 0.000 description 1
- 230000004054 inflammatory process Effects 0.000 description 1
- 238000001802 infusion Methods 0.000 description 1
- 239000003112 inhibitor Substances 0.000 description 1
- 150000002484 inorganic compounds Chemical class 0.000 description 1
- 229910010272 inorganic material Inorganic materials 0.000 description 1
- 238000003780 insertion Methods 0.000 description 1
- 230000037431 insertion Effects 0.000 description 1
- 230000017307 interleukin-4 production Effects 0.000 description 1
- 230000004068 intracellular signaling Effects 0.000 description 1
- 239000004816 latex Substances 0.000 description 1
- 150000002611 lead compounds Chemical class 0.000 description 1
- 230000000670 limiting effect Effects 0.000 description 1
- 238000010801 machine learning Methods 0.000 description 1
- 238000007726 management method Methods 0.000 description 1
- 238000004519 manufacturing process Methods 0.000 description 1
- 238000005259 measurement Methods 0.000 description 1
- 230000007246 mechanism Effects 0.000 description 1
- 108020004084 membrane receptors Proteins 0.000 description 1
- 102000006240 membrane receptors Human genes 0.000 description 1
- 230000009061 membrane transport Effects 0.000 description 1
- 210000003071 memory t lymphocyte Anatomy 0.000 description 1
- 108020004999 messenger RNA Proteins 0.000 description 1
- 230000002503 metabolic effect Effects 0.000 description 1
- 238000006241 metabolic reaction Methods 0.000 description 1
- 230000003278 mimic effect Effects 0.000 description 1
- 230000006540 mitochondrial respiration Effects 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004899 motility Effects 0.000 description 1
- 230000003843 mucus production Effects 0.000 description 1
- 210000004296 naive t lymphocyte Anatomy 0.000 description 1
- 150000002894 organic compounds Chemical class 0.000 description 1
- 230000036961 partial effect Effects 0.000 description 1
- 230000007310 pathophysiology Effects 0.000 description 1
- 238000003909 pattern recognition Methods 0.000 description 1
- 230000026731 phosphorylation Effects 0.000 description 1
- 238000006366 phosphorylation reaction Methods 0.000 description 1
- 230000035479 physiological effects, processes and functions Effects 0.000 description 1
- 210000004180 plasmocyte Anatomy 0.000 description 1
- 238000012545 processing Methods 0.000 description 1
- 230000035755 proliferation Effects 0.000 description 1
- 238000001243 protein synthesis Methods 0.000 description 1
- 238000004451 qualitative analysis Methods 0.000 description 1
- 108020003175 receptors Proteins 0.000 description 1
- 102000005962 receptors Human genes 0.000 description 1
- 230000002829 reductive effect Effects 0.000 description 1
- 238000009877 rendering Methods 0.000 description 1
- 238000011160 research Methods 0.000 description 1
- JJSYXNQGLHBRRK-SFEDZAPPSA-N ryanodine Chemical compound O([C@@H]1[C@]([C@@]2([C@]3(O)[C@]45O[C@@]2(O)C[C@]([C@]4(CC[C@H](C)[C@H]5O)O)(C)[C@@]31O)C)(O)C(C)C)C(=O)C1=CC=CN1 JJSYXNQGLHBRRK-SFEDZAPPSA-N 0.000 description 1
- 210000001908 sarcoplasmic reticulum Anatomy 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 238000013515 script Methods 0.000 description 1
- 230000007781 signaling event Effects 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- 230000002194 synthesizing effect Effects 0.000 description 1
- 230000008685 targeting Effects 0.000 description 1
- 230000002123 temporal effect Effects 0.000 description 1
- 238000003325 tomography Methods 0.000 description 1
- 238000013518 transcription Methods 0.000 description 1
- 230000035897 transcription Effects 0.000 description 1
- 238000012546 transfer Methods 0.000 description 1
- 230000001131 transforming effect Effects 0.000 description 1
- 230000014616 translation Effects 0.000 description 1
- 238000010200 validation analysis Methods 0.000 description 1
- 108700026220 vif Genes Proteins 0.000 description 1
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
- G16B50/20—Heterogeneous data integration
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Evolutionary Biology (AREA)
- Medical Informatics (AREA)
- Biophysics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Theoretical Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Databases & Information Systems (AREA)
- Bioethics (AREA)
- Molecular Biology (AREA)
- Physiology (AREA)
- Management, Administration, Business Operations System, And Electronic Commerce (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Complex Calculations (AREA)
Abstract
Les informations génétiques, biochimiques, biophysiques et anatomiques sont intégrées au niveau infracellulaire et cellulaire, au niveau du tissu et de l'organe. Au moins une base de données contenant des informations biologiques est utilisée pour générer au moins une structure de données à laquelle un attribut au moins se trouve associé. Une interface permet, de manière interactive, de visualiser, d'éditer ou de relier des attributs de structures de données pour établir au moins une description hiérarchique des fonctions infracellulaire, cellulaire, tissulaire et organique. La description hiérarchique peut être optionnellement une structure de données élémentaire, binaire ou de cheminement, ou bien encore, une structure de données anatomique pouvant être modifiée pour constituer un modèle structurel. Un calculateur génère mathématiquement au moins une structure de données à partir de la description hiérarchique. Les informations génétiques sont consultées, présentées sous forme de tableaux et combinées à des informations fonctionnelles relatives au rôle biochimique et physiologique de produits géniques. Des modèles de calcul de processus génétiques, biochimiques et biophysiques à l'intérieur de cellules et de systèmes d'ordre supérieur sont automatiquement établis, résolus et analysés sur la base de la combinaison des informations génétiques et des informations fonctionnelles ajoutées. On obtient ainsi un dispositif dynamique qui sert à réaliser des objectifs mis en évidence, tels qu'une meilleure compréhension des processus biologiques, l'identification de nouvelles cibles médicamenteuses pour l'intervention thérapeutique, et les prédictions quant aux résultats du criblage de médicaments. Ces objectifs sont réalisés par la création d'interactions dynamiques non linéaires hautement complexes qui interviennent entre chaque gène ou produit génique.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US49957500A | 2000-02-07 | 2000-02-07 | |
| US09/499,575 | 2000-02-07 | ||
| PCT/US2001/001988 WO2001057775A2 (fr) | 2000-02-07 | 2001-01-22 | Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques: in silico cell |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2399272A1 true CA2399272A1 (fr) | 2001-08-09 |
Family
ID=23985791
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002399272A Abandoned CA2399272A1 (fr) | 2000-02-07 | 2001-01-22 | Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques: in silico cell |
Country Status (6)
| Country | Link |
|---|---|
| EP (1) | EP1368774A2 (fr) |
| JP (1) | JP2004501415A (fr) |
| AU (1) | AU3649001A (fr) |
| CA (1) | CA2399272A1 (fr) |
| IL (1) | IL151070A0 (fr) |
| WO (1) | WO2001057775A2 (fr) |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7069534B2 (en) | 2003-12-17 | 2006-06-27 | Sahouria Emile Y | Mask creation with hierarchy management using cover cells |
| US7844431B2 (en) | 2004-02-20 | 2010-11-30 | The Mathworks, Inc. | Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions |
| US8554486B2 (en) | 2004-02-20 | 2013-10-08 | The Mathworks, Inc. | Method, computer program product, and apparatus for selective memory restoration of a simulation |
Families Citing this family (21)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2000046405A2 (fr) | 1999-02-02 | 2000-08-10 | Bernhard Palsson | Procedes d'identification de cibles pour medicaments a partir de donnees de sequence genomique |
| WO2000063793A2 (fr) | 1999-04-16 | 2000-10-26 | Entelos, Inc. | Procede et appareil pour effectuer des operations de simulation liees a l'aide d'un modele de systeme informatise |
| US7127379B2 (en) | 2001-01-31 | 2006-10-24 | The Regents Of The University Of California | Method for the evolutionary design of biochemical reaction networks |
| US7353152B2 (en) | 2001-05-02 | 2008-04-01 | Entelos, Inc. | Method and apparatus for computer modeling diabetes |
| CA2446865C (fr) | 2001-05-17 | 2012-07-17 | Entelos, Inc. | Appareil et procede concus pour valider un modele informatique |
| US6862561B2 (en) | 2001-05-29 | 2005-03-01 | Entelos, Inc. | Method and apparatus for computer modeling a joint |
| US7751981B2 (en) | 2001-10-26 | 2010-07-06 | The Regents Of The University Of California | Articles of manufacture and methods for modeling Saccharomyces cerevisiae metabolism |
| US20030224363A1 (en) * | 2002-03-19 | 2003-12-04 | Park Sung M. | Compositions and methods for modeling bacillus subtilis metabolism |
| US8949032B2 (en) | 2002-03-29 | 2015-02-03 | Genomatica, Inc. | Multicellular metabolic models and methods |
| CA2480216A1 (fr) * | 2002-03-29 | 2003-10-09 | Genomatica, Inc. | Modeles de metabolismes humains, et procedes associes |
| US20030220928A1 (en) * | 2002-05-21 | 2003-11-27 | Patrick Durand | Method for organizing and querying a genomic and proteomic databases |
| US7856317B2 (en) | 2002-06-14 | 2010-12-21 | Genomatica, Inc. | Systems and methods for constructing genomic-based phenotypic models |
| US7869957B2 (en) | 2002-10-15 | 2011-01-11 | The Regents Of The University Of California | Methods and systems to identify operational reaction pathways |
| US7734420B2 (en) | 2002-10-15 | 2010-06-08 | The Regents Of The University Of California | Methods and systems to identify operational reaction pathways |
| FR2854709B1 (fr) * | 2003-05-07 | 2005-08-05 | Gilbert Chauvet | Systeme et procede de simulation de l'evolution d'organismes vivants complexes |
| US7853406B2 (en) | 2003-06-13 | 2010-12-14 | Entelos, Inc. | Predictive toxicology for biological systems |
| CA2546420A1 (fr) | 2003-11-19 | 2005-06-09 | Entelos, Inc. | Dispositifs et procedes pour l'evaluation de l'utilisation de substrat metabolique |
| US10325686B2 (en) * | 2012-07-05 | 2019-06-18 | Siemens Healthcare Gmbh | System and methods for integrated and predictive analysis of molecular, imaging, and clinical data for patient-specific management of diseases |
| EP3283989A4 (fr) * | 2015-02-04 | 2018-12-19 | Rath, Matthias W. | Procédé et système permettant la visualisation en temps réel d'un état de santé d'un individu sur un dispositif mobile |
| KR102316648B1 (ko) | 2018-01-05 | 2021-10-22 | 일루미나, 인코포레이티드 | 시퀀싱 시스템에서의 시약 냉각기 불안정성 및 플로우 셀 히터 고장의 예측 |
| US11288576B2 (en) | 2018-01-05 | 2022-03-29 | Illumina, Inc. | Predicting quality of sequencing results using deep neural networks |
Family Cites Families (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5273038A (en) * | 1990-07-09 | 1993-12-28 | Beavin William C | Computer simulation of live organ |
| US5930154A (en) * | 1995-01-17 | 1999-07-27 | Intertech Ventures, Ltd. | Computer-based system and methods for information storage, modeling and simulation of complex systems organized in discrete compartments in time and space |
| US5914891A (en) * | 1995-01-20 | 1999-06-22 | Board Of Trustees, The Leland Stanford Junior University | System and method for simulating operation of biochemical systems |
| US5947899A (en) * | 1996-08-23 | 1999-09-07 | Physiome Sciences | Computational system and method for modeling the heart |
-
2001
- 2001-01-22 EP EP01908645A patent/EP1368774A2/fr not_active Withdrawn
- 2001-01-22 IL IL15107001A patent/IL151070A0/xx unknown
- 2001-01-22 WO PCT/US2001/001988 patent/WO2001057775A2/fr not_active Ceased
- 2001-01-22 AU AU36490/01A patent/AU3649001A/en not_active Abandoned
- 2001-01-22 JP JP2001556956A patent/JP2004501415A/ja active Pending
- 2001-01-22 CA CA002399272A patent/CA2399272A1/fr not_active Abandoned
Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7069534B2 (en) | 2003-12-17 | 2006-06-27 | Sahouria Emile Y | Mask creation with hierarchy management using cover cells |
| US7844431B2 (en) | 2004-02-20 | 2010-11-30 | The Mathworks, Inc. | Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions |
| US8234098B2 (en) | 2004-02-20 | 2012-07-31 | The Mathworks, Inc. | Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions |
| US8554486B2 (en) | 2004-02-20 | 2013-10-08 | The Mathworks, Inc. | Method, computer program product, and apparatus for selective memory restoration of a simulation |
Also Published As
| Publication number | Publication date |
|---|---|
| JP2004501415A (ja) | 2004-01-15 |
| WO2001057775A2 (fr) | 2001-08-09 |
| WO2001057775A3 (fr) | 2003-10-02 |
| EP1368774A2 (fr) | 2003-12-10 |
| IL151070A0 (en) | 2003-04-10 |
| WO2001057775A9 (fr) | 2003-11-27 |
| AU3649001A (en) | 2001-08-14 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CA2399272A1 (fr) | Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques: in silico cell | |
| Slepchenko et al. | Computational cell biology: spatiotemporal simulation of cellular events | |
| Demir et al. | PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways | |
| EP1171841B1 (fr) | Systeme et procede de modelisation d'informations genetiques, biochimiques, biophysiques et anatomiques | |
| Rubin et al. | National center for biomedical ontology: advancing biomedicine through structured organization of scientific knowledge | |
| US6983227B1 (en) | Virtual models of complex systems | |
| Wellstead et al. | The role of control and system theory in systems biology | |
| WO2002044992A2 (fr) | Systeme de modelisation de mecanismes biologiques | |
| Loew et al. | The virtual cell project | |
| Sekiguchi et al. | WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways | |
| Collado-Vides et al. | Modeling and simulation of gene regulation and metabolic pathways | |
| Wang et al. | Using SCDL for integrating tools and data for complex biomedical applications | |
| Mishra et al. | Simpathica: a computational systems biology tool within the valis bioinformatics environment | |
| Daigle Jr et al. | Current progress in static and dynamic modeling of biological networks | |
| May et al. | BioXyce: an engineering platform for the study of cellular systems | |
| Zimányi et al. | Semantic visualization of biochemical databases | |
| JP2007520773A (ja) | 生化学情報のための情報管理システム | |
| Kumar | Quantitative study on cellular signaling database: management and analysis of signaling network | |
| Lee | Bioinformatics Approaches for Studying Metabolic Pathways | |
| Collado-Vides et al. | Modelling and Simulation of Gene and Cell Regulation and Metabolic Pathways (Dagstuhl Seminar 98251) | |
| Nalluri et al. | Bioinformatics and Systems Biology in Bioengineering | |
| Freier et al. | iUDB: an object-oriented system for modelling, integration and analysis of gene controlled metabolic networks | |
| Chen | In silico systems analysis of biopathways | |
| Özsoyoglu et al. | Towards an Integrated Software System for Biological Pathways. | |
| Eils et al. | Databases for systems biology |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| FZDE | Discontinued |