Nextgenediting Global Initiative

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. 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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Free scientific and medical editing for authors from low income countries

Today (20th May 2013) Nextgenediting, a provider of premium scientific and medical editing services, launches the Nextgenediting Global Initiative. This free service addresses two unmet needs within the scientific editing sector: the provision of high-quality editing to authors from low- and middle-income countries (LMICs) and the provision of training for individuals seeking a career in medical and scientific editing.

Authors from LMICs face a number of barriers to scholarly communication, not least the frequently high charges associated with publishing the results of their research. Some publishers committed to open access of the scientific literature already meet the cost of publishing. However, unlike their 'first-world' counterparts, many authors from LMICs simply cannot afford the 'polish' provided by professional editing companies to help get their manuscripts published in highly competitive international journals. The Nextgenediting Global Initiative aims to remove this barrier.

Volunteer editors will edit the manuscripts submitted to the Initiative. In return for providing their time, Nextgenediting will provide these volunteers with professional feedback on their work. In addition, volunteers will have the opportunity to participate in an online training program with a focus on critical appraisal of the scientific literature, technology developments, statistical analysis, and ethics.

Company Director Sarah Aitken said: "We regularly see really high-quality manuscripts from scientists from the poorest countries, and until now we have been unable to help them. We have selected twelve talented volunteers who show a real passion to help these authors publish. The Global Initiative will ultimately help to develop local research skills and infrastructure in low-income countries and improve opportunities for inclusion in the global research agenda."

Nextgenediting is part of Nextgenology Ltd., a leading professional editing company based in the United Kingdom dedicated to improving science by providing quality editing, publishing, research, and educational services to the clinical, medical, and scientific communities.

For further information, please email: or visit
If you are an author from one of the eligible countries, you can submit your manuscript here.
If you are a publisher or journal editor who wants to find out more, or promote the initiative, please click here.


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The Nextgenediting Global Initiative - Update #2

We just wanted to post a brief update on the Nextgenediting Global Initiative.

We are now no longer accepting applications for volunteer editors. We received over one hundred applications, which was an unexpected and phenomenal response.

We have selected twelve individuals for the first phase of this exciting project, all of whom demonstrated that they have a real passion for the social aspects of the initiative, often very personally. 

We believe that we have struck the right balance in terms of experience and qualifications in the group. Half have doctorates, while the other half possess other experience or attributes which we feel will enrich the group and ultimately improve the quality of service. We believe that we can all learn a lot from each other through this diversity, and those with less experience can benefit from interacting with more experienced colleagues. Our focus will unashamedly be on the science, since we believe it is the quality of the science (and what we can do to improve it) that matters most to the successful dissemination of scientific endeavour.

We are starting to receive interest from authors from low-income countries, and we are pursuing links with publishers to improve visibility of this worthwhile cause. We aim to open our doors to submissions later this month, so please continue to let people know that this service is available and that we are eager to receive submissions.

For further information, please click here.
If you are a publisher or journal editor who wants to find out more, or promote the initiative, please click here.

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The Nextgenediting Global Initiative - Update #1

Two and a half weeks ago we launched the Nextgenediting Global Initiative, which seeks to provide free editorial services to the poorest nations. Thank you for the very positive feedback and encouragement. We would like to give you an update on how things are progressing.

The response from would-be editors has been truly remarkable. Once again we would like to say a genuine “thanks” to all the applicants - over eighty so far - and we are reviewing these in detail in order to decide on the first ten or so who will take part in the first phase of this innovative project. We will inform all applicants of the outcome by the end of March, and there is still time to apply if you would like to get involved - just fill out the application form here.

The applicants so far offer amazing breadth and depth in both qualifications and experience (from grad students to professors, from lawyers to leading medical researchers). It looks like we can build a strong and vibrant community of editors of varying experience and seniority. This will allow for peer support for junior editors, while maintaining high editorial standards and subject-specific editing. We have also been struck by several applications from individuals who originate from the Global Initiative target countries, but who are now established researchers in developed countries. These scientists in particular recognise this unmet need for editorial help in these countries, and provide a first-hand perspective on what we are trying to achieve.

In response to comments, we have started to build an online forum for the editors, which will be a shared environment for discussion. Since Nextgenediting places the science at the heart of the editing process, we will organise regular journal clubs in order to hone critical appraisal skills.

A question we have been asked a few times is “Why only ten editors?”. Firstly, we do not wish to disenfranchise either our volunteers or the authors who submit manuscripts, and by keeping the initial number of editors small we can keep a closer eye on standards. Secondly, until we have support from the larger publishers, the number of documents we receive is actually likely to be rather small.

This is where you can help. Please tell people about this, and spread the word both online and in person. Let’s encourage the use of the service, so that we can grow the mutual benefit that the Nextgenediting Global Initiative seeks to provide.

For further information, please click here.
If you would like to apply to be a volunteer editor, please click here.
If you are a publisher or journal editor who wants to find out more, or promote the initiative, please click here.

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The Nextgenediting Global Initiative

Today, Nextgenediting launches the search for volunteers for the Nextgenediting Global Initiative.

The Global Initiative aims to address two unmet needs within the scientific editing sector: the need for provision of high-quality editing to authors from low-income countries, and the provision of training for individuals seeking a career in medical and scientific editing.

Two events occurred here recently which brought home the need for innovation in this area. Firstly, we received a few manuscripts from low-income countries which were of high scientific quality. However, they required editing and the authors were unable to pay ‘high-income country’ editing fees, which represented 50-100% of their monthly wage. The second thing that happened was that Rubriq, a company based in the US, launched its portable peer review service which will see further fees passed on to the author (see a Nature news item here). This will place another barrier between the output from scientists in low-income countries, and publishing in recognised international journals. Although these developments are no doubt exciting (and indeed necessary) for those within the industry, they are also another source of global inequity in science.

We recognise that there may be a solution to this, hence the Nextgenediting Global Initiative. We receive many requests each month from individuals seeking to carve out careers in medical and scientific editing, but do not know where to start. We believe that one way to learn how to edit is by ‘on-the-job’ training, feedback, and mentorship.

By matching volunteer editors with manuscripts from low-income countries, and quality-assuring the process at Nextgenediting, we believe that we can improve the accessibility of editing services - and hence the quality of the communication of the science - without unduly harming commercial interests.

Everyone stands to gain: authors get their manuscripts improved at no cost and receive quality feedback on style and English, editors receive training, publishers receive higher-quality submissions, we meet our aims of being an ethical and socially responsible company, and society benefits from the dissemination of science which may otherwise not be published due to financial constraints or shortcomings in language and editing.

We believe that by offering these services at no cost to authors from the poorest countries, we will help remove another barrier they face in scholarly communication. The Nextgenediting Global Initiative will ultimately help to develop local research skills and infrastructure in low-income countries. This improves their chances of being included in the global research agenda.

We are currently in the first phase of the initiative - the recruitment of volunteer editors. Manuscript submission will start in April. While a core aim of the project is to support training of junior editors, we will also welcome experienced editors who wish to offer their services for free. Nextgenediting is absorbing the costs associated with the initiative, which is being offered on a non-profit basis.

For further information, please click here.
If you would like to apply to be a volunteer editor, please click here.
If you are a publisher or journal editor who wants to find out more, or promote the initiative, please click here.

Finally, please spread the word via social networking (links below or top right). This promises to be exciting.

The Nextgenediting Team

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The World Databank - An Amazing Resource

Something we feel strongly about at Nextgenediting is the use of computational biology to support and contextualise the main experimental findings of a biological paper. There is a wealth of primary research that can be performed before you even get started doing your experiments in the lab, and the best papers know how to make the best use of it. These data can be particularly useful for grant applications, too. We sometimes send recommendations back to our biomedical authors saying ‘go to GEO and analyse this dataset - you have all the information available to you tell you exactly what the expression of your gene of interest is in thousands of breast cancers…or colon cancers…or cardiovascular patients….or whatever your disease of interest is’. When you take this approach you often find the experiment you were planning (in vitro or in vivo) has already been performed, or there is supporting mouse data, or often clinical data. They can be used to generate the first figure(s) of the paper, put the experimental data in clinical context, and save a huge amount of time and effort performing costly -omics experiments. If you don’t know how to use these resources or need more information, please contact us.

What we hadn’t realised until very recently was that the same can be done for epidemiological data. We are currently planning our Nextgenediting Global Initiative (for more information click here), and while researching health and income statistics of third-world countries we found the World Bank World Databank. This is a free, online database of Development Indicators, Gender Statistics, and other useful data, which you can mine and interrogate at will for hundreds of different countries - both developed and otherwise. Most exciting for us however, is the Health, Nutrition, and Population Statistics Database which allows you to mine health and disease-related data. You just choose your country or countries of interest, the data series you want, and the range of years you are comparing (from 1961 to present) and the results are presented as tables, graphs, or on a map. You can even download the raw data and work with it yourself to present your own graphs or figures. Truly amazing.

We remember feeling like this when we first realised we could get our hands on raw gene expression data. What a powerful tool to contextualise your own work.

So if, for instance, if you are doing a study on HIV, and you need to know what the AIDS death rates are in various African countries, it would take two minutes to get this chart:

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which you can then fully customise. So much better than some outdated and over-cited WHO data, don’t you think? You can then get a first-hand grip on the numbers, trends, and associations relevant to your own research.

The World Databank provide the following video tutorial, so please check it out:

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We strongly recommend you go and have a play with this fabulous resource and see if it is useful for you. It’ll be particularly useful for students looking for thesis data. And please let us know what you think by commenting below.

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