پایان نامه بررسی کاربرد شبکه های پتری شی گرا در مدل سازی سلول

فهرست و منابع پایان نامه بررسی کاربرد شبکه های پتری شی گرا در مدل سازی سلول

فهرست:

فهرست.........................................................................................................................................................................................هشت 

چکیده ........................................................................................................................................................................................دوازده 

فصل اول .................................................................................................................................................................................................1-1-  مقدمه....................................................................................................................................................................................... 2

مدلسازی یک فعالیت طبیعی............................................................................................................................................. 3

مدلسازی در دنیای کامپیوتر............................................................................................................................................... 3

مدلسازی و بیوانفورماتیک.................................................................................................................................................. 4

طرح مساله.............................................................................................................................................................................. 5

اهداف و محدوده.................................................................................................................................................................... 5

بیانی از راه حل...................................................................................................................................................................... 5

ساختار پایان نامه.................................................................................................................................................................. 6

فصل دوم ................................................................................................................................................................................................ 7 2-1-  مقدمه...................................................................................................................................................................................... 8

2-2-   نگاهی کلان به بیوانفورماتیک و مدلسازی..................................................................................................................... 8

3-2-  زیست شناسی سیستمی..................................................................................................................................................... 8

2-4-  زیست شناسی سیستمی و مهندسی نر مافزار................................................................................................................. 9

2-5-  انتخاب نگاه...........................................................................................................................................................................10

2-6- مدلسازی ریاضی و شی گرایی در یک نگاه....................................................................................................................11

                     هشت2-7-  معرفی شبکه های پتری....................................................................................................................................................13

2-7- 1-  ساختار شبکه پتری ........................................................................................................................................................ 14

2-7- 2- علامت گذاری شبکه پتری .............................................................................................................................................. 16

2-8-  قوانین اجرا بر شبکه پتری.................................................................................................................................................16

2-9-  انواع شبکه های پتری........................................................................................................................................................17

2-9- 1- شبکه  های پتری تصادفی ............................................................................................................................................. 17

2-9- 2- شبکه  های پتری پیوسته .............................................................................................................................................. 19

2-9- 3- شبکه پتری زماندار .......................................................................................................................................................... 20

2-9- 4- شبکه های پتری ترکیبی ............................................................................................................................................... 21

2-9- 5- شبکه  های پتری خود-اصلاحی و عملکردی ........................................................................................................... 24

2-9- 6- شبکه های پتری ترکیبی عملکردی ............................................................................................................................ 25

2-9- 7- شبکه های پتری شی گرا............................................................................................................................................... 27

2-01-  شبکه های پتری در بیوانفورماتیک..............................................................................................................................39

2-11-  شبکه های پتری و شبکه های زیستی........................................................................................................................44

2-11- 1-  شبکه های بیوشیمیایی ............................................................................................................................................... 44

2-11- 2-  شبکه های ژنتیکی ......................................................................................................................................................... 46

2-11- 3-  شبکه های سیگنالی ..................................................................................................................................................... 47

2-21-  نتیجه گیری  فصل...........................................................................................................................................................48

فصل سوم ............................................................................................................................................................................................ 49 3-1-  مقدمه....................................................................................................................................................................................50

3-2-  زیست شناسی: نگاهی نزدیکتر.........................................................................................................................................50

                                                                       نه

3-2- 1-  زیست شناسی مدرن ..................................................................................................................................................... 50

3-2- 2- سلول: از بالا به پایین و از پایین به بالا ...................................................................................................................... 51

3-3-  مدلسازی پاسخی برای پیچیدگی....................................................................................................................................53

3-3- 1- سیتوپلاسم ......................................................................................................................................................................... 54

3-3- 2- غشای سلول ...................................................................................................................................................................... 55

3-3- 3- گیرندههای غشا ................................................................................................................................................................ 57

3-3- 4- شبکه آندوپلاسمی ........................................................................................................................................................... 58

3-3- 5- دستگاه گلژی .................................................................................................................................................................... 61

3-3- 6- لیزوزوم ................................................................................................................................................................................ 62

3-3- 7-  هسته ................................................................................................................................................................................. 62

3-3- 8- میتوکندری ........................................................................................................................................................................ 64

3-4-  نیازمندیهای شبکه های پتری برای مدلسازی..............................................................................................................66

3-5-  نتیجه گیری فصل...............................................................................................................................................................69

فصل چهارم ......................................................................................................................................................................................... 70 4-1-  مقدمه....................................................................................................................................................................................71

4-2-  انتخاب شبکه پتری شی گرا.............................................................................................................................................71

4-3-  بیان غیر رسمی روش پیشنهادی....................................................................................................................................73

4-3- 1- انتخاب موجودیتهای اصلی بر اساس هستان شناسی ............................................................................................. 73

4-3- 2- بدست آوردن نقشهای دخیل در شبکه های زیستی به وسیله کارتهای CRC ............................................... 77

4-3- 3- افزودن ارث بریها .............................................................................................................................................................. 78

4-3- 4-  افزودن عبارت مسیر برای محدود کردن ترتیب مسئولیتهای کارتها ................................................................. 79

ده

4-3- 5- کشیدن شبکه پتری متناسب با هر کارت برای انجام مسؤلیتها ........................................................................... 79

4-3- 6- افزودن همکاریهای هر کارت ......................................................................................................................................... 85

4-3- 7-  بازبینی مدل برای اطمینان از صحت آن .................................................................................................................. 85

4-3- 8- شبیه سازی مدل بدست آمده ...................................................................................................................................... 87

4-3- 9- به روز رسانی کتابخانه نقش .......................................................................................................................................... 89

4-3- 01-  قابلیت استفاده مجدد در مدل ................................................................................................................................... 89

4-4-  نتیجه گیری فصل...............................................................................................................................................................90

فصل پنجم .......................................................................................................................................................................................... 92 5-1-  مقدمه....................................................................................................................................................................................93

5-1- 1- رگولاسیون پروتئین G................................................................................................................................................... 93

5-1- 2- مرگ سلولی .................................................................................................................................................................... 100

5-2-  نتیجه گیری فصل............................................................................................................................................................111

فصل ششم ....................................................................................................................................................................................... 112 6- 1- مرور مراحل پژوهش........................................................................................................................................................113

6- 2- ارزیابی میزان موفقیت روش پیشنهادی......................................................................................................................114

6- 3- کاربرد روش پیشنهادی...................................................................................................................................................115

6- 4- مقایسه روش پیشنهادی با سایر روشها.......................................................................................................................115

6- 5- کارهای آینده.....................................................................................................................................................................118

ضمایم ................................................................................................................................................................................................ 119

فهرست منابع و مراجع .................................................................................................................................................................. 134

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