Tools
Where can I find the latest cancer statistics?
We receive quite a few cancer research papers to edit, and it is not uncommon for authors to set the scene by presenting a few ‘critical’ cancer facts (such as incidence, prevalence, and mortality) in the opening lines of the introduction. There is nothing wrong with this (although we wouldn’t necessarily advise it if you are submitting to a highly specialised cancer journal), but it is important that the figures are correct. We often find that the ‘facts’ are, more often than not, wildly out of date, inaccurate, or incompletely referenced. Given the easy accessibility of online data, there really is no excuse for glaring inaccuracies and any sloppiness could irritate a reviewer.
That’s why we suggest that you visit GLOBOCAN, an online resource established and maintained by the International Agency for Research on Cancer (part of the WHO). The GLOBOCAN project provides current estimates of the incidence, mortality, and prevalence of major cancer types for 184 countries. The data can be separated by sex, and 1-, 3-, and 5-year prevalence data are available for the adult population.
The database is particularly useful since it can be queried using online analysis tools, which allow you to produce graphs, tables, and maps to illustrate data. These tools are likely to be particularly useful for theses and dissertations, where there is often a need to provide more comprehensive background to the subject and provide basic data.
For instance, let’s say that you need to prepare a graph that compares age-standardised incidence and mortality rates of female cancers in ‘developed’ and ‘developing’ regions. Easy!
The graph clearly highlights those cancers that persist as first-world problems, such as breast cancer, and those cancers that more commonly affect women in the developing world (such as cervical cancer). This might provide an excellent starting point for a discussion about the epidemiology of these diseases.
GLOBOCAN can be referenced in your manuscript, and there is a useful glossary of terms, just in case you tend to get your ‘incidences’ and ‘prevalences’ mixed up. Of course, there are other excellent statistical resources available to cancer researchers, such as CRUK’s Cancer Stats resource in the UK or the NCI’s tools in the US. Please let us know if you know of any other resources that you find useful by commenting below!
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That’s why we suggest that you visit GLOBOCAN, an online resource established and maintained by the International Agency for Research on Cancer (part of the WHO). The GLOBOCAN project provides current estimates of the incidence, mortality, and prevalence of major cancer types for 184 countries. The data can be separated by sex, and 1-, 3-, and 5-year prevalence data are available for the adult population.
The database is particularly useful since it can be queried using online analysis tools, which allow you to produce graphs, tables, and maps to illustrate data. These tools are likely to be particularly useful for theses and dissertations, where there is often a need to provide more comprehensive background to the subject and provide basic data.
For instance, let’s say that you need to prepare a graph that compares age-standardised incidence and mortality rates of female cancers in ‘developed’ and ‘developing’ regions. Easy!
The graph clearly highlights those cancers that persist as first-world problems, such as breast cancer, and those cancers that more commonly affect women in the developing world (such as cervical cancer). This might provide an excellent starting point for a discussion about the epidemiology of these diseases.
GLOBOCAN can be referenced in your manuscript, and there is a useful glossary of terms, just in case you tend to get your ‘incidences’ and ‘prevalences’ mixed up. Of course, there are other excellent statistical resources available to cancer researchers, such as CRUK’s Cancer Stats resource in the UK or the NCI’s tools in the US. Please let us know if you know of any other resources that you find useful by commenting below!
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Open source software for scientists - our top five recommendations
As part of our drive to help reduce barriers to scientific publishing, today we would like to share Nextgenediting’s top five open source or free alternatives to commercial scientific software packages. Although the vast majority of the submissions we receive are written in Microsoft Word with citations embedded using Endnote, we also use the freely available programs listed below to help edit and prepare papers for submission. This has become even more important as we liaise with scientists from low- and middle-income countries as part of the Global Initiative, who sometimes cannot afford the (sometimes extremely) high cost of commercial software. Please let us know if you have any other recommendations or questions about the use of these packages.
1. Image processing and manipulation - GIMP (The GNU Image Manipulation Program)
GIMP is a fantastic and versatile alternative to Adobe Photoshop, feely downloadable for all platforms (Mac, Windows, Linux, and others). We find it particularly useful for image conversion in preparation for manuscript submission, especially for producing the high-resolution 300 dpi figures frequently required by the journals. Although the learning curve is relatively steep, there is comprehensive online documentation (including in multiple languages) that holds your hand through basic tasks, such as image re-sizing, cropping, and how to add text to figures. Although CMKY is not supported, we use the Separate+ plugin when conversion is necessary. Give it a try!
2. Statistical analysis - PSPP
Although SPSS is probably the dominant statistical analysis software package used in the social and life sciences, its high cost and annual license fees make it inaccessible to many researchers and students, particularly those already working in under-resourced environments. Although R is a phenomenally powerful (and free) statistical programming environment, it can be difficult to learn due to the lack of an intuitive graphical interface and need to grasp a new programming language (great in theory, just not going to happen in practice for most of us). PSPP is an open source alternative to SPSS that is certainly worth a shot. It is limited to basic analyses - descriptive statistics, linear regression, t-tests, and the like - but those familiar with the SPSS interface will have no problems using it since it is almost identical. If more people start to use it, perhaps we will see development of more complex functions.
3. Citation management - Bibus
Learning how to use citation management/bibliographic software is a must for academics. The proprietary software packages are not usually prohibitively expensive, but it would be wise to check with your institution first to see whether they have cheaper institutional licensing arrangements and training courses available. However, what about a free alternative? We recommend Bibus, a powerful reference management software package that integrates with MS Word and OpenOffice and allows online searching of PubMed via an intuitive user interface. One drawback though - while you can get Bibus to work on a Mac, it does not currently integrate with Word for Mac.
4. Typesetting and word processing - LaTeX
The scientific community is, without doubt, tied down to MS Word for document preparation and that is unlikely to change in the near future. The transition to any other word processing program can seem daunting, and most of us who have tried have generally failed. OpenOffice.org is a free alternative to MS Office and, as explained above, can be used with citation management software to good effect. However, LaTeX, another powerful ‘programming language’, might be worth exploring if you are embarking on a large document that requires a professional finish, such as a thesis. LaTeX produces documents with superior typesetting and is particularly useful if the document contains a lot of maths. It is free and easily extensible (see the Comprenhesive TeX Archive Network, CTAN). It does take some getting used to because it is not WYSIWYG, but consider it if you are about to undertake a ‘long-haul’ project. See also the great resource from the Department of Engineering at the University of Cambridge to help you get started with LaTeX.
5. Open Access (OA) article searching - CORE Research Mobile App (for iOS and Android)
Sometimes finding the data can be as difficult as processing it, especially when a lot of papers are still hidden behind paywalls. We recently found this nifty app from the UK’s Open University, which allows you to search and download freely available, full-text articles and read them on your device (in another app of your choosing, such as Kindle). The repository currently contains over 18 million open access articles. A great place to look if you need to find full text to support your research and don’t have access to journal subscriptions.
So there we are - our top five open source software packages for scientists - but please suggest your own too using the comments box below.
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1. Image processing and manipulation - GIMP (The GNU Image Manipulation Program)
GIMP is a fantastic and versatile alternative to Adobe Photoshop, feely downloadable for all platforms (Mac, Windows, Linux, and others). We find it particularly useful for image conversion in preparation for manuscript submission, especially for producing the high-resolution 300 dpi figures frequently required by the journals. Although the learning curve is relatively steep, there is comprehensive online documentation (including in multiple languages) that holds your hand through basic tasks, such as image re-sizing, cropping, and how to add text to figures. Although CMKY is not supported, we use the Separate+ plugin when conversion is necessary. Give it a try!
2. Statistical analysis - PSPP
Although SPSS is probably the dominant statistical analysis software package used in the social and life sciences, its high cost and annual license fees make it inaccessible to many researchers and students, particularly those already working in under-resourced environments. Although R is a phenomenally powerful (and free) statistical programming environment, it can be difficult to learn due to the lack of an intuitive graphical interface and need to grasp a new programming language (great in theory, just not going to happen in practice for most of us). PSPP is an open source alternative to SPSS that is certainly worth a shot. It is limited to basic analyses - descriptive statistics, linear regression, t-tests, and the like - but those familiar with the SPSS interface will have no problems using it since it is almost identical. If more people start to use it, perhaps we will see development of more complex functions.
3. Citation management - Bibus
Learning how to use citation management/bibliographic software is a must for academics. The proprietary software packages are not usually prohibitively expensive, but it would be wise to check with your institution first to see whether they have cheaper institutional licensing arrangements and training courses available. However, what about a free alternative? We recommend Bibus, a powerful reference management software package that integrates with MS Word and OpenOffice and allows online searching of PubMed via an intuitive user interface. One drawback though - while you can get Bibus to work on a Mac, it does not currently integrate with Word for Mac.
4. Typesetting and word processing - LaTeX
The scientific community is, without doubt, tied down to MS Word for document preparation and that is unlikely to change in the near future. The transition to any other word processing program can seem daunting, and most of us who have tried have generally failed. OpenOffice.org is a free alternative to MS Office and, as explained above, can be used with citation management software to good effect. However, LaTeX, another powerful ‘programming language’, might be worth exploring if you are embarking on a large document that requires a professional finish, such as a thesis. LaTeX produces documents with superior typesetting and is particularly useful if the document contains a lot of maths. It is free and easily extensible (see the Comprenhesive TeX Archive Network, CTAN). It does take some getting used to because it is not WYSIWYG, but consider it if you are about to undertake a ‘long-haul’ project. See also the great resource from the Department of Engineering at the University of Cambridge to help you get started with LaTeX.
5. Open Access (OA) article searching - CORE Research Mobile App (for iOS and Android)
Sometimes finding the data can be as difficult as processing it, especially when a lot of papers are still hidden behind paywalls. We recently found this nifty app from the UK’s Open University, which allows you to search and download freely available, full-text articles and read them on your device (in another app of your choosing, such as Kindle). The repository currently contains over 18 million open access articles. A great place to look if you need to find full text to support your research and don’t have access to journal subscriptions.
So there we are - our top five open source software packages for scientists - but please suggest your own too using the comments box below.
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Where should I submit my paper?
Even for experienced authors, selecting the right journal to submit a paper to can be a difficult decision. For inexperienced authors it can be downright confusing. Over the past few years the proliferation of open-access journals has resulted in more choice than ever, but as Declan Butler reports in this recent Nature article, some open-access publishers are ‘predatory’ and appear to prioritise profits ahead of scientific rigour. They are best avoided. The checklist in the Nature article is a handy guide you may wish to consult prior to submission. Briefly:
We would also add that you should check that the journal is indexed in Pubmed or other relevant indexing and abstracting services. Since new journals are not indexed immediately they may still be worth considering as a suitable ‘home’ for your paper, but in our experience the papers we edit are easily of a standard that they deserve publication in an established, high-quality journal.
Of course there are many other factors that need considering when choosing which journal to publish in. Some of these are fairly predictable, such as impact factor, cost to publish, whether it is open-access, subject-specificity, and journal scope. Some other parameters are a little more subjective and require subject-specific expertise and an intimate knowledge of the field, journals, or journal editors’ preferences. Often the work requires external and unbiased appraisal so that the authors do not fall into the trap of either pitching the article too high or too low (the latter being more common in our experience).
If you do not have access to that kind of scientific publishing support, please contact us for assistance from our own subject-specific editors. In general, we target the highest possible impact factor after scientific appraisal of your manuscript, and we aim to ensure your manuscript is actually a) accessible and b) going to be read. Otherwise, what’s the point of publishing it in the first place?
However, one of the great things about our new forum for our Global Initiative Volunteers is that there has been some sharing of useful resources. We like JANE (Journal/Author Name Estimator) in particular (thanks to Jen for this tip). JANE is a freely available web-based tool that allows you to identify suitable journals based on the title of your manuscript or other suitable keywords. It can also be used to find peer reviewers or even citations relevant to your paper that you may have missed. Since the results are given an ‘Article Influence’ score, it can help you rank the journals so you have an impact-based strategy for getting published. While no substitute for professional academic support, it certainly is an extremely useful starting point.
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- check the journal’s contact details,
- ensure the editorial board is legitimate,
- ensure the author fees are transparent prior to submission,
- beware of journals originating from spam emails,
- assess the quality of papers already published in the journal,
- ensure the journal is a member of an industry association,
- and use common sense!
We would also add that you should check that the journal is indexed in Pubmed or other relevant indexing and abstracting services. Since new journals are not indexed immediately they may still be worth considering as a suitable ‘home’ for your paper, but in our experience the papers we edit are easily of a standard that they deserve publication in an established, high-quality journal.
Of course there are many other factors that need considering when choosing which journal to publish in. Some of these are fairly predictable, such as impact factor, cost to publish, whether it is open-access, subject-specificity, and journal scope. Some other parameters are a little more subjective and require subject-specific expertise and an intimate knowledge of the field, journals, or journal editors’ preferences. Often the work requires external and unbiased appraisal so that the authors do not fall into the trap of either pitching the article too high or too low (the latter being more common in our experience).
If you do not have access to that kind of scientific publishing support, please contact us for assistance from our own subject-specific editors. In general, we target the highest possible impact factor after scientific appraisal of your manuscript, and we aim to ensure your manuscript is actually a) accessible and b) going to be read. Otherwise, what’s the point of publishing it in the first place?
However, one of the great things about our new forum for our Global Initiative Volunteers is that there has been some sharing of useful resources. We like JANE (Journal/Author Name Estimator) in particular (thanks to Jen for this tip). JANE is a freely available web-based tool that allows you to identify suitable journals based on the title of your manuscript or other suitable keywords. It can also be used to find peer reviewers or even citations relevant to your paper that you may have missed. Since the results are given an ‘Article Influence’ score, it can help you rank the journals so you have an impact-based strategy for getting published. While no substitute for professional academic support, it certainly is an extremely useful starting point.
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