Honours in the SoLES Molecular Bioscience - Semester 1 2016 Commencement

Honours Orientation Day for Semester 1 students is Wednesday, 10th February, 2016. See schedule below for details.

I. Schedule and Due Dates



Wednesday, 10th February

Honours orientation

09:15am Lvl 4 Common Room Molecular Bioscience Building G08

Welcome and overview of the honours year honours year

Thursday, 11th February

Begin fulltime work with your supervisor

Friday, 12th February

SciTech library training room: Charlotte Jabarak

Information Literacy Training (10:00am to 12:00pm)

Thursday, 18th February

Chemical Safety training course (09:30am to 13:00pm), Lvl 4 Common Room, G08

Wednesday, 24th February

Project proposal talks, New Law Seminar 022 and 028 followed by SoLES BBQ, Cadigal Green (in front of Molecular Bioscience Building G08)

Friday, 4th March

Project proposal to be submitted via eLearning website by 17:00pm

April (dates TBC)

Biostatistics tutorial sessions (11:00am to 12:30pm)

Thursday, 21st April

Submit literature review. Hard copy to supervisor and electronic submission via eLearning website by 17:00pm

Tuesday, 26th April

Coursework introductory tutorial: critical evaluation of scientific literature (14:00pm to 15:30pm)

Monday, 2nd May to 1st June

Coursework weekly tutorials, presentation of critical evaluation of a research paper. Day/time/venue will vary for each group

Tuesday, 7th June

Coursework examination (09:00am to 13:00pm)

July - August

Progress presentation to Honours panel

Thursday, 20th October

Electronic copy of thesis (pdf) to be submitted to eLearning website by 17:00pm (or emailed to Chair of Honours Committee if submission difficulty)

Friday, 21st October

3 hard copies of thesis (temporary binding) to be submitted to SoLES Academic Support Office, Building G08 by 10:00am

Monday, 31st October to Thursday, 3rd November

Thesis talks and oral examinations

Friday, 18th November

Corrected thesis due via electronic submission to eLearning website by 17:00pm

II. Course Summary

For the award of Honours, students must satisfy the following criteria:

  1. Attend the series of introductory lectures and relevant safety training sessions.
  2. Attend the SoLES Seminar Program and talks by fellow Honours students (this includes the project proposal talks and final seminars). Attendance is mandatory, independent of location of research project. Students may also be required to attend other lectures, seminars, or courses suggested by their supervisors or the Honours Committee.
  3. Present a written project proposal.
  4. Present a brief proposal talk.
  5. Carry out a research project supervised by one or more staff members.
  6. Prepare a literature review.
  7. Participate in a series of tutorials on biostatistics
  8. Participate in a series of tutorials on the critical evaluation of literature.
  9. Present an oral critical evaluation of a scientific publication.
  10. Sit a written exam on critical evaluation.
  11. Make a mid-year research progress presentation.
  12. Present a thesis based on their research project.
  13. Deliver a final talk on that project.
  14. Attend an oral examination on the thesis.
  15. Make corrections to their thesis, as directed, and submit the corrected thesis.

The Honours year requires a fulltime commitment and students should consider this when planning their study program

III. Details of the course

During the Honours year a committee broadly representative of Biochemistry and Microbiology staff in SoLES monitors the assessment and progress of each student. For the research component of your year many activities will be in subgroups that are discipline-oriented (including proposal talks, progress talks and final talks). Panels of academics with corresponding expertise will be associated with each Honours subgroup and contribute to mentorship (discuss progress, problems, etc.) and assessment for that group. These panels are chaired by the appropriate member of the Honours Committee.

In 2016 the Biochemistry and Microbiology honours committee consists of:
Andrew Holmes (Chair), Jacqui Matthews, Tim Newsome, Kim Bell-Anderson, Dale Hancock, Jill Johnston.

In 2016, for the coursework component of the year students will work in small groups of 6 to 10 students. The groups are constructed to ensure an even spread of expertise (e.g. some microbiology, structural biology and genetics) across the groups. Additional research-focussed academics are involved in these sessions such that each session is run by two to four academics from distinct disciplines.

In addition to the basic safety orientation that forms part of the Honours Orientation day, Honours students are required to participate in the following safety training programs:

  1. "WHS online induction”: All students are required to independently complete this online module. Details on how to access this induction module form part of this orientation booklet.
  2. “Working with chemicals”: All students are required to attend the Working with Chemicals training that will be held at G08 on Thursday, February 18th. You will receive information on how to register for this training by email. Should you not be able to attend the training you must independently register and complete one of the training sessions run by the University of Sydney’s Work Health and Safety unit before being permitted to work unsupervised with hazardous substances. Details on how to register form part of this orientation booklet.
  3. “Biosafety training”: students are required to independently register and complete one of the training sessions run by the University of Sydney’s Work Health and Safety unit. Details on how to register form part of this orientation booklet.
  4. Any additional training as required for the research project. This may include training in animal handling or radiation training.


PROJECT PROPOSAL TALK (10 minutes plus questions)
Each student will present a brief talk on Wednesday, 24th February detailing the background of their project and the experimental work they intend to undertake. This should be pitched for a general scientific audience.

Feedback from the Project Proposal talk will be provided to students and their supervisors from the relevant Honours Panel prior to finalizing the written project proposal.

WRITTEN PROJECT PROPOSAL (approx. 1000 words, not including references)
Each student will prepare a project proposal, which should include:

  • The background, aims and significance of the project, including an indication of the relationship of the project to the work of others, citing key references, and some discussion of the methods and techniques to be used.
  • A timeline for the proposed research.

Students should submit an electronic copy of their project proposal via the eLearning web site, by 5:00pm, Friday 4th March, 2016. These project proposal tasks are not provided a mark, but will be assessed as either Satisfactory or Unsatisfactory. Students may be asked to resubmit their proposal if unsatisfactory performance is noted.


Students will attend a short series of tutorials on Biostatistics. It is likely these will be held in April but dates are still to be confirmed. Although there will be no formal assessment during these Biostatistics tutorials, you are expected to demonstrate and apply an understanding of the presented tutorial material during the critical evaluation of scientific literature and for the coursework examination (see below).


TUTORIALS (participation in 6 tutorials)
Students will attend an introductory tutorial on the critical evaluation of scientific literature conducted by the Honours Committee Tuesday 26th April, 2016. In the subsequent 5 weeks, students will each lead or co-lead a discussion based on the evaluation of a pre-selected published manuscript. Students will be mentored in this activity by their academic group leaders. All students will be required to read the papers prior to the tutorial and contribute to discussions. Assessment (10% of the final Honours mark) will be based on the preparation/presentation (3%, see “tutorial facilitation” below) and participation (7%) in the group discussions.

TUTORIAL FACILITATION (45 minute presentation and discussion)
Each student will present a critical evaluation of a pre-selected scientific publication to their Honours group and members of the associated academic Honours panel. In this presentation the student is expected to demonstrate an understanding of the content of the article and relevant background material, interpret the data, evaluate the support for the author’s conclusions, and generate a discussion among their peers regarding the importance of the findings.

EXAMINATION (written examination)
Following the critical evaluation tutorials, students will sit a written examination to assess their ability to critically evaluate a scientific publication in a field related to their coursework tutorials. Supporting material may be provided to students one week in advance of the examination. The examination is worth 15% of the final Honours mark.


Students are required to submit a literature review to the eLearning website AND to their supervisor by 5pm, Thursday 21st April, 2016. This literature review should be viewed as forming the basis for the “Introduction” chapter of the thesis and should be consistent with the length and formatting guidelines for the thesis. A mark will not be provided for the literature review, but it will be assessed as either Satisfactory or Unsatisfactory. Feedback will be provided by your supervisor.


Students will be required to make a mid-year presentation to academics from their Honours area. The format of this presentation may vary from group-to-group, but is likely to consist of a short report or short presentation (10 minutes), and discussion. You should be able to show a completed write up of key methods and at least one Figure/Table with your experimental data by this stage. This task is not assessed. It is designed for students to discuss progress, flag any unforeseen problems and receive feedback and advice.


The preparation of the thesis, both in its format and its content, is an important part of the training of an Honours student and should be planned with the advice of the Supervisor. Students are advised that thesis writing is very time-consuming and are urged to allocate at least six weeks for this task.

Structure of the thesis

The thesis should have the following general format:

  • Title page – the full title of the thesis; full name and completed degrees of the candidate; the degree for which the thesis is submitted and a statement that the thesis is submitted in partial fulfilment of the requirements for that degree; the name of the University and Faculty; month and year in which the thesis is submitted; word count (of Introduction, Results and Discussion, including Figure legends). The university logo is not to be included for the initial submission.
  • Table of contents – list chapters, sections and subheadings only. Present a numbered list for figures and tables.
  • Acknowledgements – acknowledge all assistance from staff and others before general acknowledgements. Explain explicitly the contribution of others to the project, describe their role and make it clear which parts of the work they carried out.
  • Abstract – a concise statement describing your research project. Abstracts usually contain background, aim(s), methods, results and conclusion and must be less than 350 words.
  • Abbreviations – list of abbreviations, in alphabetical order, used throughout the thesis. Non-standard abbreviations should be defined, and should be kept to a minimum.
  • Introduction – literature review and general aims of the research project. It should cover a discussion of the current literature in the research area and how your experiments address a knowledge gap in and contribute to the field.
  • Materials and Methods – clear and detailed description of the materials and methods used in experiments and data analysis, including statistical analysis. They should follow in the style of a relevant publication in the field; standard methods can be presented with reference to the literature while any alterations to such methods should be included in sufficient detail that the experiment could be repeated.
  • Results – logical and clear presentation of all experimental results with reference to tables and figures and appropriate application of statistics.
  • Discussion – a critical discussion and interpretation of the results with reference to previous scientific studies; assessment of the limitations of the research and future directions; significance of findings within the context of the broader field of knowledge. The basis of deductions from experimental data should be clearly and succinctly explained. Readers should not need to refer to the original literature to assess the soundness of conclusions drawn from the data. It may be appropriate to combine the Results and Discussion into a single section. Seek advice from your supervisor on this matter.
  • References – reference articles from recent or seminal journal publications. Referencing should follow the format used by the FASEB journal or similar. The authors’ surnames and initials, year, title of paper, journal, volume, and first and last page numbers should be quoted. Within the text the citation should be indicated by a number in brackets. Referencing of any online resources should indicate the date they were accessed.
  • Example reference for a journal article:
    Li, L. L., Keverne, E. B., Aparicio, S. A., Ishino, F., Barton, S. C., and Surani, M. A. (1999) Regulation of maternal behavior and offspring growth by paternally expressed Peg3. Science 284, 330–333
  • Example reference for a book chapter:
    Jaken, S., and Jones, W. A. (1992) PKC interactions with intracellular components. In Protein Kinase C, Current Concepts and Future Perspectives (Lester, D. S., and Epand, R. M., eds) pp. 237-273, Ellis Horwood, Ltd., W. Sussex, England
  • Example reference for an online resource:
    Department of the Environment and Water Resources. (2007). Water resources: water for the environment. Retrieved October 21, 2014, from http://www.environment.gov.au/water/environmental/wetlands/about.html.
  • Appendices (if required) - Additional material which the student wishes to include may be presented in appendices (but all essential material should be included in the body of the thesis).
Format and presentation of the thesis
  • Paper – A4
  • Margins – 25mm top, bottom and right. 35mm left margin.
  • Font – Times New Roman, Helvetica, Calibri or Arial, 12pt.
  • Line spacing – 1.5
  • Printing – double sided
  • Thesis length – The thesis should not need to be longer than 10,000 words. There is no specific penalty mark formula for exceeding this length, but lower grades will result for inability to write concisely. The word count includes introduction, results, discussion and associated figure legends. The word count excludes the title page, student’s declaration, acknowledgements, abstract, table of contents, list of abbreviations, materials and methods, reference list and appendices.
  • Tables – must have an explanatory title and number. If the table has symbols these should be explained at the foot of the table.
  • Figures – must have a legend with title and number. All symbols must be explained in the legend. Include units of measurement and number of experiments. The legend can include additional information to explain the figure eg. brief methodology.
Helpful suggestions

To assist in preparation of the thesis, students are advised to prepare data figures and write up methods throughout the year.

The thesis is assessed by academics in related fields who should be considered knowledgeable but non-experts. This is the appropriate level and the audience for the thesis. Additionally, it should be intelligible to students and staff members working in other fields.


The complete thesis must be submitted in electronic form (pdf) using Turnitin via the eLearning website by 5pm, Thursday 20th October, 2016.

This electronically-submitted version is the official document for assessment.

If the size of the file causes difficulty with electronic submission students can either email the thesis to A/Prof Andrew Holmes () or use the University’s large file transfer facility called Cloudstor.

In addition to the electronic version, 3 hard copies of the thesis must be submitted in a temporary binding (such as comb binding or heat binding) to the SoLES Academic Support Office, located on Level 4 of the Molecular Bioscience Building by 10am, Friday 21st October, 2016. The student should also keep an additional hard copy of the thesis for use at the oral examination. The hard copies of the thesis should be accompanied by a statement signed by the student, certifying that the thesis is the result of the candidate’s own research and that it has not, nor any part of it, been submitted for a degree to any other university or institution and that the hard copy is identical to the electronic copy. A student’s declaration form will be provided.

Please note that if either the pdf or the hard copies of the thesis are not received by the specified deadlines, a mark penalty will be incurred. The penalty will be a 3% reduction per day from the thesis component (60%) of the final Honours mark.

Your research performance will be assessed by 3 examiners from the relevant clusters within School of Life and Environmental Science. Assessment is primarily based upon the thesis as an official account of your research (and your defence of the thesis in an oral exam), but will also take into account your performance in the laboratory including time management and the development of research independence. Marks from each assessor are reviewed by the Honours committee to ensure consistent application of the assessment standards.

In assessing the thesis, the examiners consider:

  • the definition of the problem;
  • the quality and interpretation of the data;
  • the amount of work that has gone into generating the data;
  • the rigour of data interpretation and justification of the conclusions;
  • the general understanding of the scientific principles underlying the problem, and its possible ramifications;
  • English expression, scientific register, correct use of referencing, layout (including word limit) and general presentation of the thesis;

Please see below ‘Range of marks in assessment’ for further details on assessment criteria. The marking rubric used for assessing Honours Performance in SoLES will also be made available to students and supervisors through the school web site and you are strongly advised to examine this when preparing your thesis.

Oral examination (usually around 30 minutes)

Each student will attend an oral examination on the work presented in the thesis and any related material that the examiners consider relevant. These discussions will be conducted by the student’s thesis examiners and will also be attended by a member of the Honours committee and the student’s supervisor.
The viva will enable the student to demonstrate that the thesis is their own work, that they understand what they have written, and that they can defend this verbally. The viva also provides an opportunity for the examiners to clarify any ambiguities in the thesis, to investigate the level of independence shown by the student in the research process and to test the student’s familiarity with how their work relates to the field of study. The viva will also enable the examiners to ascertain whether the student’s research performance may have been affected by factors including the availability of resources, disruptions to research, or other personal circumstances.
The thesis and oral examination are used together to determine the overall mark to a value of 65% of the final Honours mark.

Thesis Amendments

Following the oral examination students will be provided with a list of suggested thesis amendments. Amendments should be made to the satisfaction of the Honours supervisor. The final amended version of the thesis must be submitted to the Honours coordinator in pdf format by email or large file transfer by 5pm, Friday 18th November, 2016. Note that a University logo may be included on the cover page in this final thesis.


Each student will present a talk (20 minutes plus question time) explaining the background to and logic of their research project, the details of the project and the most important conclusions. Concise delivery of scientific material is essential and time limits will be strictly enforced. It is also important that students are able to defend their approach and conclusions during the question time after their presentation.

A panel comprised of academic staff with a diverse representation of research expertise will mark the thesis talks. As such your talk should be pitched for a general scientific audience. The talk will be assessed on the following criteria: quality of presentation, overall design and structure of the talk, scientific context and understanding, answers to questions.

The SoLES marking rubric for honours research talks will be made available to all staff and students via the school web site, you are strongly advised to examine this when preparing your talks.

Please see below ‘Range of marks in assessment’ for further details on marking criteria.

Following the oral examination (see below) students will be provided with a list of suggested thesis amendments. Amendments should be made to the satisfaction of the Honours supervisor. The final amended version of the thesis must be submitted via electronic submission to eLearning website by 5:00pm, Friday 18th November, 2016 and a hard-bound copy must also be presented to the supervisor by this time. Note that a University crest may be included in this final thesis. A promo forma coversheet for the final thesis, which includes the crest, will be provided.

IV. Assessment

1. Summary of assessment

Component % of total assessment Number of assessors

Coursework: critical evaluation of scientific literature

-          tutorial participation and contribution

-          tutorial presentation

-          examination








2 + Panel review


Research, thesis and oral examination 60% Honours panel
Thesis talk 15% 5

2. Range of marks in assessment

The University grades final Honours results according to the following scale:


 Standard  Assessment range %


 HII, Division 1


 HII, Division 2




 Not of Honours standard


Interim feedback to students may also be given according to the traditional scale, HD 85-100, D 75-84, Cr 65-74, P 50-64.

The following is a guide for interpreting Honours assessment standards:

95-100: This mark should be reserved for a student who has been outstanding in all aspects of their research. Such a student must have shown initiative and originality in their planning and execution of experiments, and independence in the analysis of results and the writing of their thesis. The mark should be reserved for students that one would confidently expect to be in the top 5% of students in any of the world's leading universities. These students will have shown such a dedication to and capacity for conducting and communicating research that one expects they will be leaders in science in the future. An outstanding H1 and clear University Medal standard.

90-94: This range should be reserved for students who have shown the highest ability but may not have performed at the top of the range in all of the categories above. This mark should identify students in the top 10% of Honours students. A possible University Medal standard.

85-89: This mark is appropriate for a student whose research performance indicates that they are capable of undertaking and completing an excellent PhD. Such students would be expected to have performed well in all areas and to have excelled in some aspects of their Honours work. A strong HI standard.

80-84: This mark should be reserved for a student who has performed at an H1 level in most aspects of their research and would be considered capable of carrying out a PhD. Such a student should have performed well in most areas, and at a satisfactory level in others.

75-79: This mark should be reserved for a student who has done a sound job in their Honours year and exhibits a solid aptitude for research. Such a student will have performed well in many but not all areas. This mark indicates that the student is probably not yet at the level of carrying out a good PhD. HII, Division 1 standard.

70-74: This mark should be reserved for a student who has performed at a satisfactory level in most areas throughout their Honours year and has done well in one or two areas. HII, Division 2 standard.

65-69: This mark should be reserved for a student whose all-round performance has been adequate for an Honours degree. Such students will have performed at a satisfactory level in most areas, or may have performed at a lower level in one or two areas but at a higher level in others. HIII Honours standard.

50-64: This mark is reserved for students who have struggled during the year and have shown a limited aptitude for research. Such students may have performed at a satisfactory level in one or two areas but overall have not performed at a standard sufficient for the award of an Honours degree.

V. Other Information

Any requests for special consideration, appeals or questions on assessment should be lodged with the Chair of the Honours committee in writing. These will be considered by the Honours Committee and the Head of School. Applications for special consideration must be made in accordance with Faculty of Science policy and procedures.

Details of the special consideration policy as applied for Honours students and applications forms are available on the Molecular Bioscience website.
The honours research program is highly individual. To ensure consistency of marks across the cohort, the application of grade standards for each component is assessed by the honours committee for consistency with undergraduate and honours coursework performances.

Following completion of all assessment tasks, the Honours Committee will meet to consider the provisional marks provided by Honours panels and will make recommendations on final marks to the Head of School and the Faculty of Science Honours Board of Examiners.

The Faculty of Science generates the SCIWAM as follows:

WAM = sum (Wi x Mi)/sum (Wi)

Where Mi is the mark obtained in course ‘i’ and the weight Wi is obtained by multiplying the unit value of the course by 2 for intermediate courses and by 3 for senior courses (results from junior units are not used in the calculation of the SCIWAM).

Unless special circumstances apply, the minimum qualification for the award of a University Medal is a SCIWAM of 80 or greater and a fourth year mark of 90 or greater. The Faculty of Science also requires evidence of sustained excellence (including prizes, awards, publications and other supporting information) to be provided by the School in support of the award of a Medal.

For the purpose of assigning Australian Postgraduate Awards, the fourth year mark out of 100 is multiplied by 1.3 and the SCIWAM by 0.7 and the total is used in the ranking.

See http://sydney.edu.au/science/cstudent/ug/wam.shtml for further information.