BIF732 - Advanced Computing Approaches

Assignment No. 03 (Graded) SEMESTER FALL 2019 BIF732- Advanced Computing Approaches Total Marks: 10 Due Date: 28-01-2020 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 Introducing FastQC: A quality assessment tool for NGS data For any query about the assignment, contact at bif732@vu.edu.pk GOOD LUCK Marks: 10 Write in your own words a paragraph comprising 5 lines about FastQC. Explain graph that is sown under the link of ‘per base sequence quality’ Link of FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Note: Solution submitted through email will also not be acceptable. Deadline: Your assignment must be uploaded/submitted on or before January 28, 2020.

Assignment No. 04 (Graded) SEMESTER Fall 2019 BIF732- Advanced Computing Approaches Total Marks: 10 Due Date: 07-02-2020 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 Introduction of R. o Learn to develop graphs in R For any query about the assignment, contact at bif732@vu.edu.pk GOOD LUCK Marks: 10 Question 1: What is R? Develop a ppt file entitled as ‘Installation Guide’ which should guide a user how to install and configure R on windows operation system. Question 2: Below are commands of R. Describe theses commands and explain each and every part of this command. msadata <- read.table(“D:\VU\Conferences\Workshops\Bioinformatics-5-01-16\R\Presentations\MSAComparison.txt”, header=T, sep=“\t”) barplot(msadata$Time, main=“Efficiency Comparison of MSA Methods”, xlab=“MSA Methods”, ylab=“Time in seconds”, names.arg=c(“T-Coffee”,“Muscle”,“Mafft”,“ProbCons”,“SATe”), border=“blue”,d=c(10,20,30,40,50)) Note: Solution submitted through email will also not be acceptable. Each question carries equal marks. Lectures Covered: This assignment covers lecture topics # 140-170 Deadline: Your assignment must be uploaded/submitted on or before February 07, 2020.

Presentation For the presentation activity, students are required to record their presentations and upload it on VULMS. MS PowerPoint allows recording audio and embedding it in a PPT file. Therefore, each student is required to prepare PPTs for his/her presentation and then record his/her voice presentation within the PPT file. Following are the guidelines in this regard: Prepare presentation slides related to any topic. There must at least 15 slides in your PPT file. First slide should contain student-ID, student-name, topic and course-name. Record your presentation using voice recorder of the Microsoft power point. The total time for recording should not exceed 5 minutes. Save your presentation slides in .ppt or .pptx format and submit on VULMS interface opened for this purpose. Double check your file before submission. If your voice is not recorded or submitted file is corrupt then you will receive zero marks. Students should submit presentation individually with their own voice recording. A guideline on how to record your presentation is uploaded in the assignment package for presentation assignment. It should be recorded in English. A good communication/ style of presenting may be awarded good marks. Objective of this assignment is to improve your soft skills. Warning: Write contents of each slide in your own words, do not copy-paste. Plagiarism is not acceptable. In case plagiarism is found, you will be awarded ZERO marks. No excuse will be accepted in this regard. For further understanding about plagiarism, please follow the links: Little Book of Plagiarism HEC Policy about plagiarism. Recording the Presentation https://www.youtube.com/watch?v=9SH5eM0914A https://www.youtube.com/watch?v=P_4x86p5dVI

Academic Research Paper Instructions As part of your course grading, you are required to submit an academic research paper during the semester. This exercise is meant to inculcate in you the research temperament and skills by carrying out a deep study of any research topic/area relevant to this course. You may choose any topic, of your interest, relevant to the course. Following are the details of academic research paper: requirements, deadlines and marks. Academic Research Paper Requirements: Following are the requirements for the academic research paper: a) Paper Length Your paper should not be less than 6 pages and not more than 12 pages. b) Quality of Writing The clarity and style of expression, the degree to which your paper obeys the rules to formal academic grammar, punctuation, spelling, formatting details like paragraph indentation and location of page breaks, are part of quality of writing. Write and edit your paper carefully for good organization, clear language with good spelling, punctuation, etc. c) Format Your academic research paper must have these sections: Abstract, Introduction, Related Work, Analysis and Conclusion. You must have to follow format (especially of writing references in the text and at end of research paper under the title of ‘References’) as described by ‘Bioinformatics’ journal strictly. The format is available at this link under the heading of ‘Manuscript Preparation’. No academic research paper will be accepted without mentioned format. d) References You must have to study published research papers (minimum 15). The references of published research papers and books are allowed. Any unauthorized materials’ references will not be acceptable. You can access Research Papers on your VULMS account using link [HEC Digital Library], Google Scholar and other online free research paper repositories (Some Journals of Bioinformatics: Nucleic Acid Research, Bioinformatics, BMC Bioinformatics, Current Bioinformatics, Evolutionary Bioinformatics etc.). Submission and Deadlines Students are required to finalize and submit their academic research paper by February 10, 2020. As the academic research paper carries 15% of the total course grade, therefore it must contain implementation results of the proposed research idea. Similarly, in case of a review paper the “Discussion” section must contain student’s comments/conclusions and future research agenda regarding the domain being reviewed. Team Students may also take this assignment in group of two (02) members/students but in that case their academic research paper must be of high quality justifying the efforts of all the members in the group. Group information (VU IDs of group members) should be sent at course email address. Warning: Write in your own words, do not copy-paste. Plagiarism is not acceptable. In case plagiarism is found, you will be awarded ZERO marks. No excuse will be accepted in this regard. For further understanding about plagiarism, please follow the links: Little Book of Plagiarism HEC Policy about plagiarism. For further information and guidelines on writing a research paper, please follow the link: Guidelines and Requirements for Writing a Research Paper