1. The Semester 2 Project Module

2. The Project Semester 2 April—September This module: the Portfolio -- background research and other preparation Design/Implementation/Experiment/Dissertation

3. This Module wk1 wk4wk6wk7wk9wk12 This lecture Hand-in portfolio Submit draft reference list: 30 relevant items Lecture 2: feedback + questions Submit skeleton draft portfolio Lecture 3: feedback + questions

4. This Module How to do really well in this module: Arrange and agree a suitable project with a supervisor Write a very, very, very good project portfolio Hand that in in week 12 (No need to come to these 3 lectures, except to find out what is required for the portfolio) (No need to provide week 4 and week 7 handins to me)

5. This Module An easier way to do very very well in this module: Arrange and agree a suitable project with a supervisor Use me, the hand-ins I ask for, and the later feedback lectures, to help you prepare the portfolio Hand that in in week 12

6. I guess you want to know what the Portfolio is?

7. The Portfolio A document of around 20 pages in total, comprising these 10 parts in this order: 1.A signed pro forma statement stating that Portfolio is free of plagiarism 2.An abstract (about 200 words) 3.Aims and objectives of your project ( about 300 words) 4.A project description, (about 500 words) 5.An appropriate discussion of the professional, legal and social issues pertinent to your project. (20—1,000 words)

8. The Portfolio 6. An outline of the dissertation structure and layout. This is expected to be presented as headings and sub headings and potentially subsub headings with a short description of the expected content of each section, sub section or subsub section. You may wish to discuss this with your supervisor. Note that this is a plan – your final report may contain a modified structure. 7. A literature review and/or review of other background material associated with your project. This is the most substantial and important component of your Portfolio -- ~5000 words or more. 8. A conclusion and discussion of the issues for your project (500—1000 words).

9. The Portfolio 9. A completed risk assessment form for your project. A risk assessment form is available from the module web site. You may not start your project until this has been completed. 10. A Project Management plan (PMP), comprising: 1. A Gantt chart outlining the timeline for the project 2. A brief description of the project plan to support the Gantt chart, to include risk identification, risk assessment and risk management.

10. Portfolio Marking Abstract, Aims, Objectives and Project description: Is the project and its rationale accurately described? Dissertation Outline: Is the project outline appropriate and well thought out? Literature Review or appropriate background material: Conclusion: Are the main issues of the project highlighted? Project Management Plan Is the PMP realistic, sufficiently detailed? Have risks been identified and assessed and has risk management been incorporated into the PMP? 10 5 60 10 15

11. You, Me, and your Supervisor For This semester only, consider me to be your main project supervisor, even if I know nothing about your project. To balance workloads over the year, student project supervision is concentrated into semester 2, when you are `actually’ doing your project. For the current background review and preparation stage, I can guide you towards producing an appropriate Portfolio, informed by the basic project description, and with a small amount of help from the supervisor.

12. An Ideal Plan for this module in this semester Weeks 2—4: Collect several pertinent reference sources on which to base your lit./background review. Use me and your supervisor appropriately to help decide what is relevant. End of week 4: Email me your list (if you want to email me your full literature review, or anything inbetween, that’s fine too) Attend week 6 lecture: in which I will give general feedback about progress so far, deal with ongoing questions about the reviews, and talk more about the other parts of the Portfolio Weeks 5—9: Organising your time appropriately, try to provide me a draft of the portfolio (skeletal in places) in week 7, and carry on drafting until week 9. Attend week 9 lecture: where I will provide general feedback on progress so far, and YOU should ask questions about what to write in particular parts of the portfolio – sometimes it is not obvious given the details of your particular project. Weeks 9—12: Finish the portfolio and hand it in.

13. One way to do a Review 1.Find 30 relevant items -- web search / google scholar / library / … -- item = seminal research paper / current research paper / website / application / system / report / perhaps your review contains some of each -- 30 is a good amount but just a guide / more may be appropriate in your case 2.Write a mini-review of each item -- 100/150 words; a description / its main features or findings, its main results and how useful they are; criticise it when it seems appropriate (cont…)

14. One way to do a Review 3.Step back and think about how to organise these reviews – what are they telling you about the state of play in the area you are looking at; the main methods, the best methods, the current directions, current progress – what seems not done yet, but seems like a good idea to try? (i.e. what are the opportunities?); what are they telling you about the best method/system/idea to use in your project? Etc etc … 4. Using your step 3 musings and your step 2 text, write a coherent review! E.g. a general introduction; a section about how the background is organised into themes and/or subthemes, a section reviewing key items in each theme, and a concluding section that pulls together generalities and makes conclusions

15. Another way to do a Review Any way that works for you, as long as leads to the same result: an organized, coherent and critically discussed account of relevant background material that sets out the context for your project, and also helps to define the project or justify aspects of it.

16. 30 items: EXAMPLE 1 Suppose this is your project  Goal: To develop a Google-type interface to bioinformatics databases  Description: The Mouse Atlas and related gene-expression databases provide both textual and spatially annotated patterns of gene-expression in the mouse and other model organism embryos. A number of specialised query interface have been developed for specific keywords, anatomical components or spatial regions. This project aims to produces a simple "google-style" interface in which the user can type any term of interest and have the search passed over complete datasets and web-site sources. The proposed architecture will be to use the Lucene (http://lucene.apache.org/java/docs/) search engine combined with bespoke links to databases to generate records in the index. In its simplest form the engine will be used to capture and index for a prescribed set of database and web-sites. An extended version of the system will allow more intelligent interpretation of a query string to include synonyms and structural relations from the anatomy and other ontologies. For example a query on "hand" will return expression patterns that are annotated with "finger" (part-of hand) or the index can be supplemented with other annotation (e.g. Gene Ontology or disease) associated with the gene. The project will require java programming coupled with delivery a of a web-application and access both to other web-sites, gene-expression databases and other bioinformatics resources. The project will take place in collaboration with the MRC Human Genetics Unit and co- supervised by Prof. Richard Baldock.

17.  Project: Develop a Google-type interface to bioinformatics databases  Foci:  google-type interfaces to databases;  Gene expression databases  Using Lucene  Coupling java with the www  Intelligent interpretation of query strings  Bioinformatics resources in general `Areas’ in this project

18.  3 sources of b/g material about java/www libraries, including Apache Lucene, but also maybe 2 others, so you can compare and contrast their features  5 online databases that have interesting/google-like interfaces;  3 online databases that have quite different interfaces, so you can contrast the two kinds.  2 key sources about gene expression data and its importance  5 sources about interpretation of query strings  12 sources about ontologies (4: definition/intro; 8: current research) 30 items might be:

19. 30 items: EXAMPLE 2 Suppose this is your project  Goal: To carry out a survey of evaluation studies which have been reported on the effectiveness of Online Learning.  Description: The project will survey the literature of evaluation studies which have been reported on the effectiveness of Online Learning. Further analysis of the context of these studies will be undertaken to produce a general report on what can be learned from these evaluations.

20.  Project: To carry out a survey of evaluation studies which have been reported on the effectiveness of Online Learning.  Foci:  Online learning  Measuring effectiveness of online learning `Areas’ in this project

21.  5 sources of b/g material about online learning itself – different styles/strategies/technologies  10 articles about evaluating the effectiveness of learning; 2 seminal, 8 recent and/or influential, 3 about offline learning, 5 about online learning.  15 studies that each present (and at least attempt to evaluate) a specifc online learning tool! 30 items might be:

22. The draft portfolio handin  WHATEVER you have ready by the end of Feb  Ideally, you will be well into the literature review part, so that I can see if the structure and organisation seems basically OK  Ideally there will be enough in the asbtract and project description parts that help me see if the project is clearly defined and you know what you are doing  At least brief notes for each section.

23. Weeks 4 and 6 wk1 wk4wk6wk7wk9wk12 Submit draft reference list at the end of week 4, email me your list of 30(ish) “items” (or, anything further towards preparing your portfolio) Lecture 2: general feedback to all, discussion of common issues. Some info about the other aspects of the portfolio, especially the PWP

24. Hand-in Dates etc. WhenWhatHow Friday 6th Feb 5pmYour 30 items on which your review will be based Email me an editable document (e.g. word, txt, not pdf) Friday 27 th Feb 5pmDraft of portfolio, maybe ~40% done, skeletal in parts Email me an editable document (e.g. word, txt, not pdf) Friday 3 rd April 5pmPortfolioPaper hand-in via the CS/IT coursework box

25. Your Questions About The `30’ items Reviews for your particular project How to do a good review Other aspects of the Portfolio