academia-aez-notes
Table of Contents
Peer review
Reviewing a resubmitted article
Here is the advice available from Wiley (accessed on 9 February 2023).
How to review revised manuscripts
It is uncommon for a paper to be accepted for publication without changes – most papers are revised at least once in light of comments from reviewers and editors.
When a revised paper is received:
- Minor changes will usually be assessed directly by the editor
- If significant revisions were requested, the editor will usually return the manuscript to the original reviewers (unless they opted out of this)
- Rarely, the editor may invite comments from a new reviewer – the editor should explain why this fresh review is sought. It is important new reviewers respect previous review comments and the efforts the author has made to revise the paper
Ideally, any significant changes should already have been requested in the original review – this subsequent review should be to ensure that the changes have been made, rather than for raising additional issues.
Thus your review of a revised manuscript should be relatively quick and may only involve checking that certain requested actions have been done. Nevertheless, the aim of the review remains the same: to ensure the paper is of a publishable standard.
Usually the editor will provide both the original decision letter and the author’s response to it. This will allow you to see what changes were requested – including any by the other reviewer – and how the author has responded to those changes.
You should focus on how the author has changed the paper in light of their own response comments. Some journals require authors to highlight the changes in their revised manuscript, which simplifies this.
Research Centres
MACSYS
ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems aims to deliver the mathematics required to compute life. The Centre will deliver innovation in computational and mathematical biology and establish in silico biology alongside in vivo and in vitro biology. These models will allow us to understand the complexity of life at the cellular level and enable new ways of combining diverse and heterogenous data. This will allow us to understand the mechanisms underlying cellular behaviour, and to apply rational design engineering methods in order to control the dynamics of biological systems.
People
- Prof. Michael Stumpf
SPARK
SPARK is an extension of SPECTRUM.
SPARK is aimed at strengthening preparedness in the Asia-Pacific region through knowledge, under the ASEAN-Pacific Infectious Disease and Response program (APIDDaR).
It uses quantitative methods and modelling to strengthen regional capacity, develop innovative tools for adaptive decision making to inform disease prevention control and elimination.
People
- Prof. Jodie McVernon
SPECTRUM
A Centre of Research Excellence aimed at enhancing national and regional decision making to improve the control of infectious diseases, strengthen health systems and reduce these risks in Australia and the Asia Pacific region through collaboration, partnerships and model-based evidence to aid decision making.
People
- Prof. Jodie McVernon
- Prof. Emma McBryde
- Prof. James McCaw
- Dr Nic Geard
Funding
Research Innovation and Commercialisation (RIC)
Research Management System (RMS)
The RMS is a web-based system to manage grant applications pertaining to the ARC. You have to register an account and then everything is meant to go through this portal.
Discovery Early Career Researcher Award (DECRA)
Timeline
Projects run for 3 years.
| Applications open | 19/10/2022 |
| Applications close | 15/12/2022 |
| Rejoinders | 30/03/2023 |
| Announcements | Late 2023 |
Hardware pricing
| Model | Price | RAM | Processor |
|---|---|---|---|
| Light weight Windows Laptop | $2845.25 ex GST | 16GB | 11th Generation Intel Core i7 |
| CTO MacBook Pro 14" Touch ID | $3162.82.00 ex GST | 16GB | M2 Pro with 10-Core CPU, 16-Core GPU |
| ThinkPad X1 Carbon Gen 9 | $2351.21 ex GST | 16GB | 11th Generation Intel Core i7 |
Academic journals
Selecting a journal
The journal citation reports are a good source of high level information about different journals. If you have trouble authenticating for this database, you can access Web of Science which provides a link to the citation reports.
Elsevier also offers a journalfinder search engine. The FAQ suggests it works based on the words in the abstract.
Journal notes
Biometrics
Not to be confused with the similar (but older) journal, Biometrika.
Published on behalf of the International Biometric Society, Biometrics emphasises the role of statistics and mathematics in the biosciences. Its objectives are to promote and extend the use of statistical and mathematical methods in the principal disciplines of biosciences by reporting on the development and application of these methods. A centrepiece of most Biometrics articles is scientific application that sets scientific or policy objectives, motivates methods development, and demonstrates the operations of new methods.
bioRxiv
To access the Author Area visit this URL: https://submit.biorxiv.org/
Epidemics
Elsevier page for Epidemics and here is the editorial board.
Epidemics
The Journal on Infectious Disease Dynamics
Editors-in-Chief: Dr. Katia Koelle, Professor Steven Riley, Dr. Cecile Viboud
GENETICS
Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work.
The editorial team
GENETICS provides an overleaf template Overleaf latex template for typesetting articles and has integrated with both Cold Spring Harbour and FigShare so there are natural choices for preprinting and how to make additional data available. Materials are to be deposited to FigShare via the GENETICS submission portal.
For an initial submission the manuscript can be in any format, although they advise that line and page numbers should be included.
PLOS Computational Biology
For papers submitted to the Methods section there are some additional requirements of the cover letter.
- Submissions
- Double spaced with a single column
- LaTeX submissions
For some reason there are different requirements for manuscripts being submitted from latex.
- Use their template
- Do not include figures in the manuscript
- References sit within the
.texfile (see my bibtex notes on how to do this) - Use Unicode characters instead of LaTeX commands when possible
- Do not include figures in the manuscript PDF. Submit figures as separate TIFF or EPS files. Figures with multiple panels (subfigures) should be uploaded as a single file. Do not upload each panel/subfigure separately.
PLOS Global Public Health
Scientific Data
Scientific Data publishes descriptions of scientifically valuable datasets under its primary article-type, the Data Descriptor.
Taken from the author guidelines.
- Tables
There are some rules regarding the use of tables
Generally, Data Descriptors, Analyses and Articles should have fewer than ten tables, but more may be allowed when needed. Tables may be of any size, but only tables that fit onto a single printed page will be included in the PDF version of the article (up to a maximum of three, see below).
…
Due to typesetting constraints, tables that cannot be fit onto a single A4 page cannot be included in the PDF version of the article and will be made available in the online version only. Any such tables must be labelled in the text as 'Online-only' tables and numbered separately from the main table list e.g. 'Table 1, Table 2, Online-only Table 1' etc.
Statistical Science
The central purpose of Statistical Science is to convey the richness, breadth and unity of the field by presenting the full range of contemporary statistical thought at a moderate technical level, accessible to the wide community of practitioners, researchers and students of statistics and probability.
Ranks high in the "Statistics & Probability" category according to Journal Citation Reports
Statistics in Medicine
Systematic Biology
Systematic Biology is the bimonthly journal of the Society of Systematic Biologists. Papers for the journal are original contributions to the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things. A Points of View section offers a forum for discussion, while book reviews and announcements of general interest are also featured.
Impact Factor 10.408 Evolutionary Biology 5 out of 50
Theoretical Population Biology
Editor-in-Chief is Noah Rosenberg of Stanford
An interdisciplinary journal, Theoretical Population Biology presents articles on theoretical aspects of the biology of populations, particularly in the areas of demography, ecology, epidemiology, evolution, and genetics. Emphasis is on the development of mathematical theory and models that enhance the understanding of biological phenomena.
Miscellaneous
Finding my FWCI
Log into Scopus via the university library.
UoM Research Computing Portal
https://rcp.research.unimelb.edu.au/home/
The Linux Researcher Desktop provides a small personal server similar to a decent laptop (top-end when boosted). You can also create an Activity and then reserve more powerful hardware for that activity. Then when you create a Research Server you can request that it uses this fancier hardware.
ISO 4 abbreviations
Information and documentation – Rules for the abbreviation of title words and titles of publications.
| ISO 4 | Journal |
|---|---|
| Am. Stat. | The American Statistician |
| Annu. Rev. Stat. Appl. | Annual Review of Statistics and Its Application |
| J. Am. Stat. Assoc. | Journal of the American Statistical Association |
| Nat. Clim. Change | Nature Climate Change |
| Nat. Commun. | Nature Communications |
| Nat. Comput. Sci. | Nature Computational Science |
| PLOS Comput. Biol. | PLOS Computational Biology |
| PLOS Glob. Public Health | PLOS Global Public Health |
| Proc. Natl. Acad. Sci. U.S.A. | Proceedings of the National Academy of Sciences of the United States of America |
| Trends Microbiol. | Trends in Microbiology |
| Trends Genet. | Trends in Genetics |
Socio-Economic Objectives
2020 Socio-Economic Objectives (SEO)
| 190499 | Natural hazards not elsewhere classified |
| 200404 | Disease distribution and transmission (incl. surveillance and response) |
| 200406 | Health protection and disaster response |
Field of Research
Field of Research (FoR) codes used in Australia and New Zealand to classify scholarly works. Here are some that apply to me.
| 490102 | Biological mathematics |
| 490303 | Numerical solution of differential and integral equations |
| 490501 | Applied statistics |
| 490502 | Biostatistics |
| 490503 | Computational statistics |
| 490505 | Large and complex data theory |
| 490507 | Spatial statistics |
| 490508 | Statistical data science |
| 490510 | Stochastic analysis and modelling |
| 490511 | Time series and spatial modelling |
| 460106 | Spatial data and applications |
| 460807 | Information visualisation |
| 461306 | Numerical computation and mathematical software |
| 310201 | Bioinformatic methods development |
| 310203 | Computational ecology and phylogenetics |
| 310207 | Statistical and quantitative genetics |
| 420202 | Disease surveillance |
| 420204 | Epidemiological methods |
| 420205 | Epidemiological modelling |