LIMS Project: Myocardial Infarction Final Report

Transcription

1 LIMS Project: Myocardial Infarction Final Report By Imran Iqbal (Project Leader) Zeeshan Khaliq Uttej Chowdary Kevin raju Group 1 Page 1

2 Acknowledgements We would like to thank Kjell Osborn and Robert Kajic for their support and for the discussions which helped us develop the ideas put forward here. We also thank Dr. Rizwan for his valuable advice on the requirements and the design of the project. Group 1 Page 2

3 Table of Contents 1. Introduction Purpose Problem Background Methodology Tools and Technologies Procedure Aim User Requirements Functional Requirements Non Functional Requirements Use case Admin: Technician: Doctor: Database Design Implementation Initial Project Plan Achieved Project Deadlines Test cases Summary Conclusion Comments of Client Future Work Group 1 Page 3

4 1. Introduction Laboratory Management Information System (LIMS) is an automated information system for tracking and managing laboratory samples, projects, analyses, measuring instruments, and quality control information, and for generating reports to clients. LIMS enable laboratories to manage their data and distribute the results to designated area. Apart from aiding regulatory compliance, LIMS can also provide benefits through improved quality of data, faster turnaround of more accurate data and automatic generation of exception reports; being able to disseminate this new-found quality data to management makes for faster decision-making. This together with the ability to dynamically update manufacturing systems and remove potential areas for error and provides tangible benefits that can be measured. 1.1 Purpose This is the Final Project Report of Group 1, Bioinformatics, submitted for the fulfillment of LIMS project done on Feb Mar This report provides a complete description of all the functions and the specifications of the project 'Myocardial Infarction'. The idea behind the project was provided by Dr. Rizwan who wanted a LIMS system to assess the early risk factor of Myocardial Infarction. The requirements were in turn developed by us and after confirmation from the client the LIMS system was developed. 1.2 Problem Background Myocardial infarction or also known as heart attack is the interruption of blood supply to a part of the heart causing heart cells to die. If left untreated for a sufficient period of time, it can cause damage or death of heart muscle tissue. When a large amount of heart muscle dies, the ability of the heart to pump blood to the rest of the body is diminished, and this can result in heart failure. This results in failure of other organs like kidneys. There are many risk factors which can cause myocardial infarction. Some of these being gender, age, level of physical activity, smoking, blood pressure, family history of Ischaemic heart disease (IHD), past history of IHD, family history of Diabetes Mellitus (DM), past history of DM, Body Mass Index (BMI ), blood HDL (High Density Lipoproteins) and Blood Triglycerides (cholesterol). Even though family history and male gender are genetically determined, the other risk factors can be modified through changes in lifestyle and medications. These factors individually or in a combination can help to determine the risk of having myocardial infarction in a person. Group 1 Page 4

5 1.3 Methodology Agile method was used for this project as the client was not sure regarding the requirements and this method gave us the flexibility to leave important decisions until more or better data was available. The various options available by using the agile method kept the project moving without fear of reaching a sudden standstill. The increments were shown to the client who reviewed it and in turn instructed the necessary changes to be done. For development of the LIMS system extreme programming was used. Extreme Programming is a discipline of software development based on values of simplicity, communication, feedback, and courage. It works by bringing the whole team together in the presence of simple practices, with enough feedback to enable the team to see where they are and to tune the practices to their unique situation. In extreme programming there are 12 types of practices that can be followed, of which we used pair programming. In pair programming all code is created by two people working together at a single computer Both programmers concentrate on the code being written. This increases software quality without impacting time to deliver. Although 2 people working at a single computer will add as much functionality as two working separately, it will be much higher in quality. 1.4 Tools and Technologies PHP (Hypertext Preprocessor) SQL(Structured Query Language) CSS (Cascading Style Sheets) HTML Dream weaver Javascript Group 1 Page 5

6 2. Procedure 2.1 Aim To assess the early risk factors of Myocardial Infarction through LIMS. 2.2 User Requirements Functional Requirements Admin Module The Admin should be able to add the fields for the technician and the doctor so that the details of the patient can be recorded in the system and viewed. The admin will have full access to the system. Admin 1 The Admin should be able to login to the system. 2 The Admin should be able to log out of the system. 3 The Admin should be able to add physical activity factor as a risk factor 4 The Admin should be able to add family history of IHD/atherosclerosis as a risk factor 5 The Admin should be able to add family history of diabetes mellitus as a risk factor 6 The Admin should be able to add past history of IHD as a risk factor 7 The Admin should be able to add history of DM as a risk factor 8 The Admin should be able to add smoking as a risk factor 9 he Admin should be able to add Blood Pressure as a risk factor 10 The Admin should be able to add BMI (Kg/m2) as a risk factor Group 1 Page 6

7 11 The Admin should be able to add blood HDL (High density lipoproteins) as a risk factor 12 The Admin should be able to add blood Triglycerides (cholesterol) as a risk factor Technician Module The technician should be able to add the patient details into the system and add the patient assessment information. Technician 1. The technician should be able to login to the system. 2. The technician should be able to logout of the system. 3. The technician should be able to add patient information. 4. The technician should be able to add patient assessment information 5. The technician should be able to search patient by name. 6. The technician should be able to search by SSN. 7. The technician should be able to search patient by Doctor Module The doctor should be able to view the report and get the summary of the report on the patient detail. Doctor 1. The doctor should be able to login to the system. Group 1 Page 7

8 2. The doctor should be able to logout of the system. 3. The doctor should be able to view the patient detail. 4. The doctor should be able to search a patient by name. 5. The doctor should be able to search a patient by name. 6. The doctor should be able to search a patient by SSN. 7. The doctor should be able to search a patient by Non Functional Requirements Compatibility The system should be compatible with Windows 2000, XP and Vista Security The password that is stored in the system should be encrypted and made sure it is inaccessible even to the system owners Usability The system should be handled by minimum of 5 persons and their reviews should be recorded regarding the system. If important the reviews should be taken into consideration and incorporated into the system Scalability Proper comments should be added with the code as any future user would be able to understand and add other function to the system Speed The system should respond to the user request within 3 seconds. Group 1 Page 8

9 2.3 Use case Admin: Entering patient information: Identified Actors Admin Actors Description Actors name Description Admin Entering patient information Admin login/logout Login/logout Actors name Description Admin Admin have to login in to the system while adding data Group 1 Page 9

10 Entering factors for blood pressure Factors Add blood pressure ADMIN Measurements Use case id use case name Ud_ad_01 Entering factors for blood pressure Actors: Description: Preconditions: Post conditions: Admin Admin add the blood pressure Admin must be logged in to the system The blood pressure received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Group 1 Page 10

11 Entering factors for blood triglycerides Factors Add blood triglycerides admin Measurements Use case id use case name Ud_ad_02 Entering factors for blood triglycerides Actors: Description: Preconditions: Post conditions: Admin Admin add the blood triglycerides Admin must be logged in to the system The blood triglycerides received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Group 1 Page 11

12 Entering factors for smoking Factors Add smoking admin Measurements Use case id use case name Ud_ad_03 Entering factors for smoking Actors: Description: Preconditions: Post conditions: Admin Admin add the smoking Admin must be logged in to the system The smoking received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Entering factors for HDL Factors Add HDL admin Measurements Group 1 Page 12

13 Use case id use case name Ud_ad_04 Entering factors for hdl Actors: Description: Preconditions: Post conditions: Admin Admin add the hdl Admin must be logged in to the system The hdl received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Entering factors for BMI Factors Add BMI admin Measurements Use case id use case name Ud_ad_05 Entering factors for BMI Actors: Description: Preconditions: Post conditions: Admin Admin add the BMI Admin must be logged in to the system The BMI received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Group 1 Page 13

14 Entering factors for physical activity Factors Add physical activity admin Measurements Use case id use case name Ud_ad_06 Entering factors for physical activity Actors: Description: Preconditions: Post conditions: Admin Admin add the physical activity Admin must be logged in to the system The physical activity received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Entering factors for IHD Factors Add IHD admin Measurements Group 1 Page 14

15 Use case id use case name Ud_ad_07 Entering factors for IHD Actors: Description: Preconditions: Post conditions: Admin Admin add the IHD Admin must be logged in to the system The IHD received from the report assign factors and measurements Normal Flow: Alternative Flows: Exceptions: Frequency of Use: admin separates the factors and allocates points Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently 4.2 Technician: Technician login/logout Login/logout Technician Actors name Description Technician Technician have to login/logout of the system Group 1 Page 15

16 Entering patient information NAME ADD P.NUM E.MAIL Technician ADDRESS Use case id use case name Ud_TE_01 Entering patient information Actors: Description: Preconditions: Post conditions: Technician Technician adds the patient details Technician must be logged in to the system The basic information about the patient is entered in to the system Normal Flow: Alternative Flows: Exceptions: Frequency of Use: Technician separates the attributes and fix it to the particular one Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Group 1 Page 16

17 Patient detail Gender Blood pressure Blood triglycerides Patient detail Physical activity Hdl Technician IHD smoking Diabetes BMI Use case id use case name Ud_TE_02 Patient detail Actors: Description: Preconditions: Technician Technician adds the patient details Technician must be logged in to the system Group 1 Page 17

18 Post conditions: The factors and measurements can be assigned by the technician Normal Flow: Alternative Flows: Exceptions: Frequency of Use: Technician can fix the measurements and factors according to the report Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently Patient search Name Search patient Pnum Technician Use case id use case name Ud_TE_02 Search patient Actors: Description: Preconditions: Post conditions: Technician Technician searches the patient by name and pnum Technician must be logged in to the system The technician search for details of the patient Normal Flow: Alternative Flows: Exceptions: Frequency of Use: Technician can search on the easier way he finds Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently 4.3 Doctor: Doctor login/logout Group 1 Page 18

19 Login/logout Doctor Actors name Description doctor doctor have to login/logout of the system Patient search Name Search patient by Pnum Doctor Use case id use case name Ud_do_01 Search patient Actors: Description: Preconditions: Post conditions: doctor Doctor can searches the patient by name and pnum Doctor must be logged in to the system The doctor search for details of the patient Normal Flow: Doctor can search on the easier way he finds Alternative Flows: Required test is not conducted in any Lab. Exceptions: Connection error. Group 1 Page 19

20 Frequency of Use: Wrong Lab test ID generated. Frequently Viewing report and progress Gender Blood triglycerides Report and Progress Physical activity Hdl Doctor IHD smoking Diabetes BMI Use case id use case name Ud_do_02 Viewing report and progress Actors: Description: Preconditions: Post conditions: doctor Doctor can view the report and progress of a patient Doctor must be logged in to the system The doctor search the patient and views the patient details Normal Flow: Doctor can search on the easier way he finds Group 1 Page 20

21 Alternative Flows: Exceptions: Frequency of Use: Required test is not conducted in any Lab. Connection error. Wrong Lab test ID generated. Frequently 2.4 Database Design Group 1 Page 21

22 Group 1 Page 22 Patient PK Patient_id Name Address Personal_Number FK1 P_ass_id FK2 User_id Datetime Pre_assessment PK P_ass_id Patient_id Pysical_activity IHD Diabetes History_IHD Smoking Blood_Pressure BMI HDL Blood_Triglycerides FK1 Pre_assement_result_id Datetime Physical_activity PK P_activity_id Measurements_name Factor FK1 P_ass_id IHD PK IHD_id Measurements_name factor FK1 P_ass_id Diabetes PK Diabetes_id Measurements_name factor FK1 P_ass_id Smoking PK Smoke_id Measurements_name factor FK1 P_ass_id Blood_Pressure PK Blood_pressure_id Measurements_name factor FK1 P_ass_id BMI PK BMI_id Measurements_name factor FK1 P_ass_id HDL PK HDL_id Measurements_name factor FK1 P_ass_id Blood_Triglycerides PK Blood_id Measurements_name factor FK1 P_ass_id Pre_assessment_result PK Pre_assement_result_id P_ass_id Result Datetime User PK User_id username password user_type FK1 User_type_id User_type PK User_type_id Designation

23 3. Implementation 3.1 Initial Project Plan S.No Deliverables Deadline 1. Requirement Analysis 12 Feb Front end design and database design 16 Feb Development of both admin and front side + Documentation 28 Feb Testing and refinement + Test report writing 3 Mar Fixing errors If any occurs 5 Mar Project demonstration to client 7 Mar Achieved Project Deadlines S.No Deliverables Deadline Achieved Requirement Analysis Achieved Front end design and database design Achieved Development of both admin and front side + Documentation Testing and refinement + Test report writing Achieved Partially Achieved Fixing errors If any occurs Achieved Project demonstration to client Achieved Group 1 Page 23

24 3.3 Test cases Test Case Product: LIMS Release 1.0 Test Case: Blood pressure Test Case-ID: TC-0001 Approved: Yes Description/Goal: To verify that User is able to save blood pressure Record. Pre-conditions for this test case: Access to form of blood pressure. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering blood pressure. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter blood pressure measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 24

25 Test Case Product: LIMS Release 1.0 Test Case: Blood triglycerides Test Case-ID: TC-0002 Approved: Yes Description/Goal: To verify that User is able to save blood triglycerides record. Pre-conditions for this test case: Access to form of blood triglycerides. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering blood triglycerides. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter blood triglycerides Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 25

26 Test Case Product: LIMS Release 1.0 Test Case: Smoking Test Case-ID: TC-0003 Approved: Yes Description/Goal: To verify that User is able to save smoking record. Pre-conditions for this test case: Access to form of smoking. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering smoking values. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter smoking measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 26

27 Test Case Product: LIMS Release 1.0 Test Case: HDL Test Case-ID: TC-0004 Approved: Yes Description/Goal: To verify that User is able to save HDL record Pre-conditions for this test case: Access to form of HDL. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering HDL. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter HDL measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 27

28 Test Case Product: LIMS Release 1.0 Test Case: BMI Test Case-ID: TC-0005 Approved: Yes Description/Goal: To verify that User is able to save BMI record. Pre-conditions for this test case: Access to form of BMI. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering BMI. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter BMI measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 28

29 Test Case Product: LIMS Release 1.0 Test Case: Physical Activity Test Case-ID: TC-0006 Approved: Yes Description/Goal: To verify that User is able to save physical activity record. Pre-conditions for this test case: Access to form of physical activity. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering physical activity. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter physical activity measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 29

30 Test Case Product: LIMS Release 1.0 Test Case: IHD Test Case-ID: TC-0007 Approved: Yes Description/Goal: To verify that User is able to save IHD record. Pre-conditions for this test case: Access to form of IHD. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering IHD. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1 Enter IHD measurement Accepted 2 Enter factor Factor value accepted Test Case Status Group 1 Page 30

31 Test Case Product: LIMS Release 1.0 Test Case: Patient Form Test Case-ID: TC-0008 Approved: Yes Description/Goal: To verify that User is able to save patient form.. Pre-conditions for this test case: Access to form of patient form. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering patient form. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result 1. Enter patient name The name is accepted. (if different from expected) 2. Enter personal no. The personal no. is accepted. 3. Enter id The id is accepted. 4. Enter address The address is accepted. Group 1 Page 31

32 5. Click on save The values are saved and are displayed in the form. Test Case Status Test Case Product: LIMS Release 1.0 Test Case: Patient Detail Test Case-ID: TC-0009 Approved: Yes Description/Goal: To verify that User is able to save patient detail.. Pre-conditions for this test case: Access to form of patient detail. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Entering patient detail. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) 1. In the Gender field, select a value from the drop down list 'Male', 'Female' The value is selected Group 1 Page 32

33 2. In the Blood pressure field, select a value from the drop down list '90-119/60-79mmHg', ' /80-89', ' /90-99', '>160/>100'. 3. In the Blood triglycerides field, select a value from the drop down list '<150 mg/dl', ' ', ' ', ' ', '>500', The value is selected The value is selected 4. In the Diabetes field, select a value from the drop down list 'none', 'first degree relatives', '2nd degree relatives'. The value is selected Group 1 Page 33

34 5. In the HDL field, select a value from the drop down list '>60 mg/dl', '51-59', '41-50', '<40'. 6. In the IHD field, select a value from the drop down list 'None', 'Yes' 7. In the Smoking field, select a value from the drop down list 'none', 'very occasional', '<5 cigarettes a day', '5-15 cigarettes a day', '>15 cigarettes a day' 8. In the Physical Activity field, select a value from the drop down list 'atleast 1h/d, 3d/wk', 'atleast 1h/d,2d/wk', 'atleast 1hr a week', 'occasionaly', 'very rare'. 9. In the Body Mass Index field, select a value from the drop down list '18-24', '25-26', The value is selected The value is selected The value is selected The value is selected The value is selected Group 1 Page 34

35 '26-28', '>30'. 10. Click on save The patient detail is saved in the database Test Case Status Test Case Product: LIMS Release 1.0 Test Case: Patient Search Test Case-ID: TC-0010 Approved: Yes Description/Goal: To verify that User is able to perform a patient search Pre-conditions for this test case: Access to form of patient search. Date: 5 Mar 2010 Use Case Reference: Environment: MS Windows Internet Explorer 6.0 Scenario: Perform patient search. Test Case: Tester: Imran Iqbal Sr.# Step Description Expected Result Actual Result (if different from expected) Group 1 Page 35

36 1. Click on 'Search Patient By Name' The form appears 2. Enter patient name The patient name is accepted 3. Click on Search The patient detail is retrieved 4. Click on 'Search Patient By SSN' The form appears 5. Enter Personal No. The personal no is accepted. 6. Click on Search The patient detail is retrieved 7. Click on 'Search Patient By ' 8. Enter the address The form appears The address is accepted 9. Click on Search The patient detail is retrieved Test Case Status Group 1 Page 36

37 4. Screen shots 4. Screen shots Screen shot of main page Screen shot of login page Group 1 Page 37

38 Screen shot of contact us Screen shot of Admin main page Group 1 Page 38

39 Screen shot of Blood pressure Screen shot of Blood Triglycerides Group 1 Page 39

40 Screen shot of Smoking Screen shot of HDL Group 1 Page 40

41 Screen shot of BMI Screen shot of Physical Activity Group 1 Page 41

42 Screen shot of IHD Screen shot of technician main page Group 1 Page 42

43 Screen shot of patient form Screen shot of patient detail Group 1 Page 43

44 Screen shot of searching patient by name Screen shot of searching patient by SSN Group 1 Page 44

45 Screen shot of searching patient by Screen shot of Patient report Group 1 Page 45

46 Screen shot of Patient Progress Group 1 Page 46

47 5. Summary 5.1 Conclusion The primary goal of the project was to develop a LIMS system for myocardial infarction where the probability of occurrence of the disease was calculated using the various risk factors associated with it. This was achieved through our LIMS system. The system was able to provide an interface for the admin and technician to enter the patient details and the doctor to print out a report regarding the lab details of the patient. 5.2 Comments of Client The client was happy with the system and wanted to incorporate a Print option configured on the final report page so that the doctor can directly take a printout. 5.3 Future Work The following are the points that can be a part of future system. 1. The future work would include a graphical representation of the report that is printed out to the doctor. 2. Many other diseases can be included in the system so that the doctor can take decisions according to the report. Group 1 Page 47