SEMESTER Fall 2019
BIF731- Advanced Bioinformatics Total Marks: 10
Due Date: 05-02-2020
Instructions
Please read the following instructions carefully before solving & submitting assignment:
It should be clear that your assignment will not get any credit ( get zero marks) if:
o The assignment is submitted after due date.
o The submitted assignment does NOT open or file is corrupted.
o The assignment is copied (from other student or ditto copy from handouts or internet).
o Submit your solution within due date. Don’t wait for grace day. Grace Day is given only if there is any problem with LMS on due date. Note that no assignment will be accepted through email if there is any problem on grace day.
Objective
The objective of this assignment is:
o Understanding I-Mutant
For any query about the assignment, contact at bif731@vu.edu.pk
GOOD LUCK
Marks: 10

What is I-Mutant for? Write a step by step tutorial (with screen shots) on using this tool. It can be opened by clicking following link.

http://folding.biofold.org/i-mutant/i-mutant2.0.html

Note:

1. Solution submitted through email will also not be acceptable.
2. Each question carries equal marks
   Lectures Covered: Link given above
   Deadline: Your assignment must be uploaded/submitted on or before February 05, 2020.

SEMESTER Fall 2019
BIF733- Bioinformatics I (Essentials of Genome Informatics) Total Marks: 10
Due Date: 05-02-2020
Instructions
Please read the following instructions carefully before solving & submitting assignment:
It should be clear that your assignment will not get any credit ( get zero marks) if:
o The assignment is submitted after due date.
o The submitted assignment does NOT open or file is corrupted.
o The assignment is copied (from other student or ditto copy from handouts or internet).
o Submit your solution within due date. Don’t wait for grace day. Grace Day is given only if there is any problem with LMS on due date. Note that no assignment will be accepted through email if there is any problem on grace day.
Objective
The objective of this assignment is:
Learning FASTQ format
For any query about the assignment, contact at bif733@vu.edu.pk
GOOD LUCK
Marks: 10

Question 1: FASTQ is a text file commonly used to store sequencing data, particularly generated from Illumina and Ion Torrent platforms. You are instructed to write a comprehensive but concise (not more than of two pages) tutorial on FASTQ format. Explain each line of this format in your own words.

Note:

1. Solution submitted through email will also not be acceptable.
2. Each question carries equal marks.
   Deadline: Your assignment must be uploaded/submitted on or before February 05, 2020.

Teaching Practice (EDUB519)
Assignment Lesson Plan (Fall 2019)
Total Marks: 30

Objective:
To assess the students’ understanding of concepts of teaching and enable them for implementing lesson planning practically.

Instructions:

• Late assignments will not be accepted.
• If the file is corrupt or problematic, it will be marked zero.
• Plagiarism will never be tolerated. Plagiarism occurs when a student uses work done by someone else as if it was his or her own; however, taking the ideas from different sources and expressing them in your own words will be encouraged.
• No assignment will be accepted via e-mail.
• The solution file should be in Word document format; the font color should be preferably black and font size should be 12 Times New Roman.

List of Activities

From 3rd week to till end of teaching practice, lesson plans and teaching will be assessed in classroom.

1. Student- teachers need to prepare two lesson plans for each subject in a week. Lesson plan needs to be submitted on weekly basis (Total 6 in a week).
   i.e. Subject 1 = 2 lesson plans
   Subject 2 = 2 lesson plans
   Subject 3 = 2 Lesson plans
   Total lesson plans = 6

2. For EDUB519 (Week 6) teaching practice, you will prepare 6 lesson plans on different topics in this assignment. Subjects should be same as mentioned in School selection form.

3. You need to upload the 6 lesson plans in a single Word Doc. File on LMS within the due date. However, you must start each lesson plan from a NEW PAGE of the solution file. DO NOT start a fresh lesson plan from the middle or end of a page.

4. An “observation tool to evaluate student-teacher” is also given in this file. Please take the print and get signed it filled, stamped and signed along with the date from your cooperating-teacher. This tool will be filled by the cooperating teacher on weekly basis.

5. You may request any of the cooperating teachers observing your class to fill the form for you. Only ONE copy of “Activity 2” from any class level is required along with 6 lesson plans.

6. Paste the scanned copy of the complete and filled “Observation tool to evaluate student-teacher” at the end of the assignment file.

7. Carefully check all 6 lesson plans and the filled scanned Activity 2 before uploading on LMS.
   Note: You have to teach the all six lessons in class and request your cooperating teacher to provide feedback on it.

8. Also fill the following table:

Activity 1: Format of Lesson Planning
Lesson plan should be activity based for students so that they can directly participate in the process of learning and construct learning from their own experiences. Here are the brief contents of the lesson plan; you may please prepare your lesson accordingly.

1. Subject

2. Grade level/ Class

3. Text Book

4. Topic & Sub Topic

5. Time duration

6. General Objectives (see sample lesson plan)

7. Specific/Instructional Objectives (see sample lesson plan assignment , use Measureable verbs to state specific objectives e.g. See Bloom’s Taxonomy)

8. Resources/Materials A.V aids (resources that will be used in the lesson)

9. Procedure
   a. Introduction (something to get the students’ attention)
   b. Teaching Procedures (methods you will use in the classroom & black/whiteboard work)
   c. Student Participation (how will you get the students’ participation)
   d. Formative check (check students’ understanding during the lesson)
   e. Closure/summarizing (how will you end the lesson)

10. Assignment or Homework (relevant to the specific objective of the lesson)

11. Assessment of Student Learning (Propose the questions for this lesson e.g. objective & subjective)
    Activity 2: Observation Tool to Evaluate Student-Teaching
    Respected Cooperating Teacher, you are requested to please give your feedback on the student-teacher teaching in the classroom. Please observe the activities of the student-teacher summed up in the following categories as mentioned in the observation checklist.
    The feedback you provide on the student-teacher teaching is measured at the following scale: Good, Satisfactory, Poor. Please observe the student-teacher on the lesson he / she has prepared and provide your valuable feedback on the following tool.
    Name of Cooperating Teacher: ______________________________
    Student-teacher Name: ____________________________________
    Class level observed: ___________________ Subject: _________________
    Date of the class observed: _____________________ Class time & duration: _____________
    Lesson topic of the class observed: _____________________________________________
    School Name & City/Dist.:____________________________________________________
    Contact No. of Cooperating Teacher/School: _____________________________________
    Teacher’s Personal Affect Observation Poor Satisfactory Good

12.  Vocal Delivery			
    

13.  Eye Contact			
    

14.  Gestures / Facial Expressions			
    

15.  Body Movement			
    

16.  Word Selection is according to students’ mental level			
    

17.  Acceptance of students’ Ideas			
    

Classroom Management Observation: Teacher Movement and Verbal Involvement Poor Satisfactory Good

1.  Teacher asks questions from students in the class 			
   

2.  Teacher responds to the questions of the students 			
   

3.  Teacher focuses on less active students			
   

Teacher’s Observation during giving a task / activity Poor Satisfactory Good

1.  Teacher clearly instructs the task			
   

2.  Students understand the task			
   

3.  Teacher answers the questions relating to the task			
   

4.  Students perform the task as desired			
   

Student Engagement Observation: Verbal Involvement Poor Satisfactory Good

1.  Teacher directs the questions to all students			
   

2.  There are only few students who respond			
   

3.  There is no difference in how the students are called upon			
   

Feedback of the Lesson Planning Poor Satisfactory Good

1.  Teaching techniques and materials used are sufficient			
   

2.  Teaching techniques and materials used are appropriate			
   

3.  The materials and teaching techniques help address different learning styles			
   

4.  Lesson plans creates interest in the students			
   

5.  Lesson plan allocates time for different activities			
   

Feedback on Teaching Poor Satisfactory Good

1.  The teacher had command on the content			
   

2.  The ideas were expressed appropriately			
   

3.  Explanation of the topic was given where needed			
   

4.  Relevant examples were shared when needed			
   

5.  Questions of students were answered properly			
   

6.  The teacher summarized the lesson			
   

7.  Feedback from students was taken in terms of questioning / answering			
   

8.  Homework related to the classwork was assigned			
   

9.  Teacher had the basic assessment plan of the topic			
   

Student-teacher sign: ___________
Cooperating –Teacher Sign: _______________
Date: ______________
Stamp of School:________________________

Assignment 4

Teaching Practice (EDUB519-II)

Assignment Lesson Plan (Fall 2019)
Total Marks: 10

Objective:
To assess the students’ understanding of concepts of teaching and enable them for implementing lesson planning practically.

Instructions:

• Late assignments will not be accepted.
• If the file is corrupt or problematic, it will be marked zero.
• Plagiarism will never be tolerated. Plagiarism occurs when a student uses work done by someone else as if it was his or her own; however, taking the ideas from different sources and expressing them in your own words will be encouraged.
• No assignment will be accepted via e-mail.
• The solution file should be in Word document format; the font color should be preferably black and font size should be 12 Times New Roman.

List of Activities

• Co-curricular activities are integral part of teaching-learning process. Students-teacher is requested to organize and participate in any three co-curricular activities on weekly basis.

Co-curricular Activities
The purpose of these activities is to take part in co-curricular activities in school.
Assembly
Please observe assembly (one per week) and share your views on this activity. You can also conduct assembly (if school allows you).

1. Write the steps involved in conducting the assembly?

2. What is the role of assembly for students’ grooming?

Reflection: What things you can improve while conducting assembly?

Recess Duty
Observe this activity (one per week) in school and record your observations against each statement.
Activity Yes, No
Any comments
Teachers were present for observation of students’ behaviors in canteen or in playground

Teachers maintained the discipline during break

Social interaction of students is positive

Which things did you observe while performing break duty? Share your experience.

Other Non-Teaching Activities
What other non-teaching activities you perform during teaching practice? (e.g. Sports Day, Bazm-e-Adab, Fun Fair, Parents-Teacher meeting, Debates etc)

Student-teacher sign: _____________________ Cooperating –Teacher Sign: ______________
Date: ___Stamp of School:

Fall2019 MCM619 Assignment 04
Be very careful while uploading your proposal as you shall not be able to replace it once uploaded.
Plagiarism is strictly prohibited. Any evidence of plagiarism (if found) shall be strictly dealt as per “ZERO TOLERANCE POLICY” of the University. (Read the Plagiarism Sensitization Document available in the DOWNLOADS section of the course VULMS).

Dear Students
You are required to send assignments on your approved/ revised topics for research. This assignment must include previous assignments as well. Your assignment must clearly state your research topic, statement of problem, objectives of the research and hypotheses/ research questions.
It is compulsory that you all must write your approved thesis title on your assignment files, only then the supervisor can finalize and guide about your methodology.
This assignment particularly requires writing the research methodology of your thesis.

Methodology explains how you design your research. What specific methods will you acquire for data collection and how it will be done. Some major headings that must be a part of your thesis are:
• Methodology
• Design
• Research Method
• Population
• Sampling Technique
• Sample size
• Instrumentation—instruments/ tools used for the data collection
• Validity and reliability of the tools/ questionnaires
• Time frame
You are required to complete this assignment by giving details of all of these sub-headings.
NOTE: Please attach your proposed questionnaires/instruments for approval. Without approval of instruments you cannot collect data.

1. Prepare presentation slides related to your academic research paper.
2. There must not be more than 20 slides in your PPT file.
3. First slide should contain student-ID, student-name, topic and course-name.
4. Your presentation should describe the problem statement, methodology and conclusion.
5. Save your presentation slides in .ppt or .pptx format.
   Video Recording:
6. You have to formally present the slides with proper dress code and have to record the video of your presentation.
7. You can use any video recording facility such as web cam, camera, mobile phone etc. for recording of your presentation (Download link of the tutorial “Tips for Recording Videos” is provided in the assignment package).
8. The total time for recording should not exceed 10 minutes.
9. After recording your video, you have to convert it in “.3gp” format using any video conversion tool to reduce the size of the video file. (Download link of the tutorial “Video Compression” is provided in the assignment package).
10. After converting the video in .3gp format, review your file to verify that audio and video are playing properly.
11. Install VLC media player to view your compressed video before uploading on VU-LMS. You can download VLC from http://www.videolan.org/vlc/download-windows.html.
12. It is preferable to use English in your presentation in case of reluctance you can also use Urdu language.
13. Note that you will record your presentation standing in front of camera.
14. Students writing academic paper in group should submit presentation individually with their own video recording.
    Submission:
15. Compress your video file and presentation file using any compression tool like WinZip or WinRAR.
16. Upload the compressed file (.zip or .rar) on VU-LMS. Make sure that its size should not exceed 30 MB.

Note: It is not required to show PPT slides in the recorded video.

Tips for Recording Videos:
http://vulms.vu.edu.pk/Courses/CS701/Downloads/Tips for Recording Videos.mp4

Video Compression:
http://vulms.vu.edu.pk/Courses/CS701/Downloads/Video Compression.mp4

1. Prepare presentation slides related to your academic research paper.
2. There must not be more than 20 slides in your PPT file.
3. First slide should contain student-ID, student-name, topic and course-name.
4. Your presentation should describe the problem statement, methodology and conclusion.
5. Save your presentation slides in .ppt or .pptx format.
   Video Recording:
6. You have to formally present the slides with proper dress code and have to record the video of your presentation.
7. You can use any video recording facility such as web cam, camera, mobile phone etc. for recording of your presentation (Download link of the tutorial “Tips for Recording Videos” is provided in the assignment package).
8. The total time for recording should not exceed 10 minutes.
9. After recording your video, you have to convert it in “.3gp” format using any video conversion tool to reduce the size of the video file. (Download link of the tutorial “Video Compression” is provided in the assignment package).
10. After converting the video in .3gp format, review your file to verify that audio and video are playing properly.
11. Install VLC media player to view your compressed video before uploading on VU-LMS. You can download VLC from http://www.videolan.org/vlc/download-windows.html.
12. It is preferable to use English in your presentation in case of reluctance you can also use Urdu language.
13. Note that you will record your presentation standing in front of camera.
14. Students writing academic paper in group should submit presentation individually with their own video recording.
    Submission:
15. Compress your video file and presentation file using any compression tool like WinZip or WinRAR.
16. Upload the compressed file (.zip or .rar) on VU-LMS. Make sure that its size should not exceed 30 MB.

Note: It is not required to show PPT slides in the recorded video.

Tips for Recording Videos:
http://vulms.vu.edu.pk/Courses/CS701/Downloads/Tips for Recording Videos.mp4

Video Compression:
http://vulms.vu.edu.pk/Courses/CS701/Downloads/Video Compression.mp4