Contents of This Site I Like archive:

August 2010

May 2010

February 2010

August 2009

May 2009
 
For the current issue's article, please go to the This Site I Like page.

August 2010

Untangling the chemical web with ChemSpider: a new search engine community for chemists from the Royal Society of Chemistrywww.chemspider.com

ChemSpider is the latest evolution of  web-based search tools from the Royal Society of Chemistry. It aims "to  aggregate into a single database all chemical structures available within open  access and commercial databases and to provide the necessary pointers from the  ChemSpider search engine to the information of interest."
At first glance the search tool itself  is pretty comprehensive, trawling multiple commercial and public databases to  provide the latest, impressively large, range of data associated with each  compound, from basic properties to predicted properties, from patents based  around that molecule to suppliers of the compound, as well as spectroscopic  data and journal articles.
  Although it is initially rather clunky  and non-intuitive (possibly the nature of a database that is trying to collate  so much varied data in a coherent way), attempts have been made to make it more  user friendly, such as explanations of key identifiers and a help manual.
However, what we have here is more than  just a search tool. With links to Wikipedia wherever possible, ChemSpider has  embraced the community - editing generation into which it has been born, and  rightly so - ChemSpider encourages the  ethos of Wikipedia by allowing members to upload new data and supplement  existing data with their own information. Enabling chemists to network and  build their professional knowledge and connections, with a real-time  interactive tool, might just be this tool's most important function.
It is also nice to see that biochemical  structures are well represented. With the modern move towards interdisciplinary  networking and information sharing becoming ever more important, a developing  database ought to reflect this, and this one does.
ChemSpider's setup, with its open  access, interdisciplinary, and community editable content, all point towards a  very forward-thinking way of developing a repository, which should help it  develop into a very comprehensive and even more useful tool than it already  looks to be.
What should they aim to include next?  Add information on existing molecules from other forms of spectroscopic  analysis, particularly from x-ray crystallography? Expand the catalogue to  include larger molecules such as full proteins? Or introduce connections  between compounds in the database in the form of reaction pathway information  (X + Y = Z )?
Though its logo might hark back to the  bygone days of early computer game graphics, this search tool is far from  dated. ChemSpider is adopting the most modern of approaches. We look forward to  seeing the next generation of developments.
 

Kate Whittaker
kfwhittaker@gmail.com
Elizabeth Milway
elizabeth.a.milway@gmail.com

Nurse Author & Editor
www.NurseAuthorEditor.com

Nurse Author & Editor, published by Wiley-Blackwell,first appeared in 1991 as a  print publication with inaugural editor and publisher Suzanne Hall Johnson.  Now, it is published online at www.NurseAuthorEditor.com. The publication is  free to subscribers and appears quarterly. One registers online and with a user  name and password can access issues of the publication from 2006, and can sign  up for alerts of the next issue posting via email.
Nurse Author & Editor is edited by Charon Pierson, who assumed the role in 2008. Dr Pierson also is the editor of the Journal of the American Academy of Nurse Practitioners. Articles  focus on writing for publication, strategies to avoid rejection of manuscripts,  locating opportunities for publishing, peer review of manuscripts, and the  editing and publishing processes.
An  international editorial board supports the publication. Authors too provide an  international perspective. The March 2010 issue (vol 20, no 1), features topics  such as:

•     Developing qualitative research  analyses
 
•     Detecting and preventing plagiarism  in publishing
 
•     Peer review: good for all purposes?

In  addition to the publication, the website hosts pages exclusively for authors,  reviewers, and editors. On the authors' page, subscribers are invited to access  the Writing for Publication booklet written by Christine Webb (2009).  Articles targeted toward authors include:

 
• You use APA  and I use AMA
 
• Secrets of successful writers
 
• The role of editors as mentors.
   

The  reviewers' section features an invitation to access the Guidebook for  Manuscript Reviewers, written by Charon Pierson and published by Blackwell  in 2007. Articles for reviewers include:

 
• Peer review survey 2009
 
• Make your voice heard: how to present  editorial comments verbally
 
• Best review practices: support nurse  authors with compassionate critique.

The  editors' page provides a listing of articles that may be of use to both novice  and experienced individuals, such as:

 
• Citation behavior
 
• Self-reflection along the path to  writing, reviewing and editing
 
• Getting nurses to write: conducting  writing for publication workshops.
   

Although  it is devoted to nursing, the publication contains content of value to other  professionals as well, whether in health care or not. Nurse Author & Editor is a useful reference on a variety of topics and can save a busy  editor a lot of time. It's also a "must read" for editorial board members and  other manuscript reviewers.
Since Dr Pierson's appointment, the publication has  undergone some changes, not least of which is the international perspective.  The website offers many useful, free features, the best of which is probably  the Journals Directory. This directory offers in one convenient location a listing  of all nursing journals, both in the US and internationally, with the editor's  name and email address listed, as well as access to the journal's Information  for Authors.

Belinda E Puetz
Editor-in-Chief, Journal for Nurses in  Staff Development
BEPuetz@aol.com

May 2010

Scientific Red Cards: a collaborative website for better communication between scientists and institutions about misconduct

Scientific publications are a basis on which to build scientific  knowledge. They also constitute a platform for decision-making in policy  formulation - for example, those concerning public health and the environment.  The reliability of the scientific record is therefore critical both for the  progress of science and for decision-making. However, the history of scientific  research provides numerous cases of misconduct. How informed is the research  community about the publications that result from misconduct, and how does it  deal with this issue?
As PhD students concerned about some social/political issues related to  science, we became interested in the debate about genetically modified organisms.  When we confronted contradictory publications, we noticed that there were  informal claims calling into question the integrity of some of these  publications. We then realised that institutions exist that are able to  investigate and identify fraudulent publications but that information about the  reliability of publications is not readily available, as the official  information from the institution is not connected to the publication itself.
It has been repeatedly noted that identification of publications that  result from misconduct is difficult. [1-6] Once an institution has  assessed a case of scientific misconduct, the corresponding articles can be  retracted. However, not all fraudulent papers get retracted, [2-4] and  retracted papers sometimes get cited after retraction.4-6 This  points to a lack of visibility of fraudulent publications.
On the one hand, this lack of visibility is a matter of connecting  pieces of information together. Some institutions able to assess misconduct put  their reports on line (the Office of Research Integrity, at the US Department  of Health and Human Services, for example). However, this information is not  well connected to the publication itself: while bibliographic content becomes  easier to access day by day, such metadata about publications are still absent  from most search engines.
On the other hand, this lack of visibility might be related to the  reluctance of the scientific community to talk about issues of misconduct.  Indeed, misconduct damages the image of scientific institutions. [7] The  possibility to debate and become informed about misconduct within the  scientific community could be beneficial.
 
Objectives
The objectives of the project are to help the identification of  fraudulent papers in the literature, and to build an environment where  scientific integrity is openly debated.
We propose to build a database available on a website; it will contain  publications in which the content has been shown to be incorrect, as a result  of misconduct.
In addition, it is important that this database be presented in a  context where people can become informed and discuss scientific integrity. [8] We  propose an interactive platform to offer information and an exchange of ideas  on this issue.
 
The project
The project is called Scientific Red Cards and is available at www.scientificredcards.org.  It has four components: a database; a blog with the possibility to comment and  debate cases; information about scientific integrity and links; and a form for  reporting assessed cases of misconduct.
The database - Each entry in the database comprises the citation  for the publication (title, authors, journal, volume, year), together with a  link to the corresponding assessment(s) of misconduct. We propose to classify  publications into three categories: fraudulent data - fabrication,  falsification, and plagiarism; non-complying publication - ignoring editorial  policies and standards (non-disclosure of conflict of interest, undeserved  authorship, for example); and unethical practices - ignoring ethical rules  (lack of informed consent of patients in clinical trials, for example).
Assessment of misconduct by validated authorities - Assessments should be made by committees  dedicated to scientific integrity, who are able to make investigations, and who  are located in research institutions and universities. The list of sources of  assessments is present on the website. Ideally, institutions would get involved  in this project and themselves guarantee the correctness of the assessment  available.
A collaborative tool - This database is designed as a collaborative tool:  any member of the scientific community can submit publication data for anything  questionable, together with a link to the corresponding assessment of  misconduct. This reference is then submitted for moderation. If it fits the  requirements (as explained above) it is included in the database.
A place for interaction - The website hosts a blog, which offers the  possibility for users to leave comments on each blog post, and users can  comment on each publication and the related assessments in the database.

A dynamic project, bound to be improved
Who carries it out? - So far, we have developed this project as PhD  students, and we have decided to make it collaborative. However, in the longer  term we believe that this project needs to be carried out by authorities with  higher legitimacy, such as institutions where research is conducted or managed,  or that deal directly with scientific misconduct (for example, research  integrity offices, editors). This would facilitate updating of the database and help to involve all  actors of the scientific community in a joint effort. Identifying who could  become involved in such a project is still an open question, but could include  research institutions, editors, and publishing associations.
What about the author responsible for  misconduct and the co-authors? - Misconduct associated with  a paper is expected to cast a shadow over the authors, not only the person  responsible for misconduct, but also the co-authors. This is a difficult point.  The names of the authors could be hidden in the database, but this would seem  hypocritical, as this information is easy to obtain from the internet. This  suggests that it would be more relevant to leave the authors' names available,  but to specify the person responsible for the misconduct. However, this is not  always easy when it comes to undisclosed conflict of interest or undeserved  authorship. Finally, in order to avoid users focusing on the names of the  authors, one possibility is to make items available only through a search tool  by topic, and to hide the full list of publications.
What code of conduct should be adhered to? - Codes  of conduct differ among countries and between institutions within countries.  However, for serious cases of misconduct, such as fabrication, falsification,  and plagiarism, they don't differ much, except perhaps in the way that  incidences of misconduct are handled and in the corresponding penalties. There  are now committees working on harmonizing these codes of conduct,10 for instance  in Europe and in the US (with the Office of Research Integrity). This process  takes time, and one can even doubt whether a common code can be formulated, as  legislation is often cultural. However, as research is international, we need  to be practical, and therefore we propose to refer to the codes of conduct of  the institution for each case.
 

To what extent is this project viable?
From a  legal point of view, the first question that emerges from our proposed project  is that of defamation. It is important to note that this database focuses on  the content of the publication, and not on the quality of the authors. In  addition, as explained above, any publication refers to a judgement already  made by an authority.
More  generally though, how does this project fit into a legal framework? So far, the  website is hosted in France, and therefore falls under French legislation. The  main point raised is that of the legal status of a scientific publication as  personal information. Indeed, handling personal information, and making such a  database available, is not straightforward. However, a scientific publication  is an item of personal information that impacts the scientific community and  beyond. Based on this, how can it be considered in the same way as personal  information?
Outreach - From a practical point of  view, this database cannot be exhaustive. In addition, this service is not  meant to address the question of errors in scientific research although it can  have a strong impact on public health policy (see Greenberg [9] for an example  of the unfounded authority of a theory due to citation bias). These points  question the relevance of this database. However, the existence of such a  database, enriched by the platform we propose to promote exchange, has a great educational  value, and a high potential for raising awareness of the issue of scientific  integrity within the community. Moreover, our first steps stand as a proof  of principle that it is technically and legally feasible to collect such  information and provide it on an integrated platform, and this should be  regarded as a milestone for institutions willing to engage in better management  of research integrity.
Despite  these questions, we are convinced that this project is both feasible and  valuable. Information on scientific misconduct must be available, both for the  scientific community and society. In addition, it remains very important that  researchers, editors, and research institutions work together to address the  issue of scientific misconduct. A dialogue, via collaborative online tools,  meetings, and written communication, is essential for any rule or guideline to  be considered and accepted by the community.
All  authors made equal contributions to the work presented here.

References

 
1. Couzin J, Unger K. Scientific misconduct. Cleaning up  the paper trail. Science 2006; 312:38-43.
 
2. Sox HC, Rennie D. Research misconduct, retraction, and  cleansing the medical literature: lessons from the Poehlman case. Annals of  Internal Medicine 2006; 144:609-613.
 
3. Schiermeier Q. Authors slow to retract 'fraudulent'  papers. Nature 1998;393:402.
 
4. Trikalinos NA, Evangelou E,  Ioannidis JP. Falsified  papers in high-impact journals were slow to retract and indistinguishable from  nonfraudulent papers. Journal of Clinical Epidemiology 2008; 61:464-470.
 
5. Gabehart ME. An analysis of citations to retracted  articles in the scientific literature. 2005. http://www.ils.unc.edu/MSpapers/3050.pdf  [accessed 29 October 2009].
 
6. Whitely WP, Rennie D, Hafner AW. The scientific  community's response to evidence of fraudulent publication. The Robert Slutsky  case. JAMA 1994; 272:170-173.
 
7. Titus SL, Wells JA, Rhoades LJ. Repairing research  integrity. Nature 2008; 453:980-982.
 
8. Committee on Assessing Integrity in Research  Environments, National Research Council, Institute of Medicine. Integrity in  scientific research: creating an environment that promotes responsible conduct. http://www.nap.edu/openbook.php?isbn=0309084792 [accessed 29 October 2009].
 
9. Greenberg SA. How citation distortions create  unfounded authority: analysis of a citation network. BMJ 2009;  339:2680.
 
10. Boesz C,  Lloyd N. Collaborations: investigating international misconduct. Nature 2008;  452:686-687
    
       
     

Timothée Flutre, Thomas  Julou, Livio  Riboli-Sasco, Claire Ribrault
PhD students, Université P  Descartes, Institut National de la Recherche Agronomique, Ecole Normale  Superieure, France
contact@scientificredcards.org

February 2010

Initially,  I tried organizing them by author. Then I tried organizing them by discipline  or subject - but then what do you do with author A who produces work in  subjects B and C? Finding that vital piece of information among all those PDFs  can be a slow and frustrating process as you search and open various files.
Mendeley is a new, free, piece of software which aims to solve all these problems (http://www.mendeley.com). It includes  desktop software for PDF archiving, a research management system for all your  references, and a linked website for collaboration and networking.
 
The desktop
The  desktop software runs on Mac, Linux, and Windows and is the main PDF archiving  and reading section of the system, allowing users to build up a "research  library" or database. Mendeley takes vital details from imported PDF files for  indexing and organization (and will notice if there are any duplicates). This  metadata can be used to create citations and bibliographies via a plug-in for  Microsoft Word or a Bibtex export facility.  If Mendeley has problems reading the PDF file, it will automatically search  PubMed, CrossRef and the DOIs, or you can direct it to search online. Out of  the 150 files I imported, about 40 needed review (to say "yes that's correct")  and only about 20 needed manual entry.
If  you don't have the PDF of the article, you can still import the citation  information manually, via online facilities, or from other research management  software such as Zotero and EndNote. Once files and references have been  archived, they can be added to personal collections, with multiple tags for  future filtering. This definitely solves that multi-disciplinary filing issue!
In  addition, you can do a full-text search within and across all available files.  Mendeley has its own tabbed reader for viewing, where the PDFs can be  highlighted and annotated.
 
The website
Users  can synchronize their desktop library to their Mendeley website profile,  uploading only the citation reference, or the PDF file as well. This provides a  back-up facility and access to your library whenever you are away from your  desktop - very useful when you are at a conference or meeting. You don't need  to worry about privacy issues, as you are the only one who can access your  online library and information - unless you choose to put some references or  papers in a shared collection - which is   when the fun really starts.
 
Sharing and network facility
Shared  collections can be managed on both the desktop and on your website profile. You  can put papers in these collections and then invite colleagues  to see, highlight, and annotate them, and add  more. The Mendeley website also acts as a social networking site, where you can  search for and connect with scientists in your field.

Downsides
I  had a few initial problems with Mendeley. Most of these would have been solved  if there had been more extensive documentation. The software is still in  development, and thus has a few things to iron out. The experience would be  improved with a better facility to merge libraries across multiple desktops,  and notification of locations of duplicate files. The initial read of your PDF  files and the website syncing facility can be quite slow. Thus, I recommend  syncing fairly regularly as you make changes. The system would also be improved  if it was more independent of this internet syncing facility, and if there was  a version of the site tailored for mobile phones.
 
Finally
Several  new and old research management systems are available (http://en.wikipedia.org/wiki/Comparison_of_reference_management_software).  These include Papers for Mac, which can archive and search PDF files (http://mekentosj.com/papers/) and  Zotero, which is a FireFox extension allowing you to collect, manage, and cite  your research sources (http://www.zotero.org/). However, only Mendeley seems to  provide both a research management and a web collaboration tool. The software  is free, but not open-source. Additional features will be introduced on a  user-pays system.
Mendeley  is still in development, and it seems that bugs are fixed very quickly. The  website encourages constant feedback via direct bug reports and separate  software improvement suggestions. This means that there are always exciting new  features on the horizon. For example, they plan to introduce a feature where  Mendeley recommends papers based on your library's contents - what a fantastic  way to keep abreast of all the exciting research out there. Personally, I feel  this software could revolutionize the way I do my science.

Emma E Doyle
Postdoctoral  fellow, Massey University, NZ
emmadoyle79@gmail.com

August 2009

Notes from the blogosphere

As a blogger since 2006, approaching my 1000th post, I'm interested in what's going on in the corner of the blogosphere that's concerned with editing and related subjects. Reading blogs is a good way to keep your finger on the pulse, to find out what's new and what the latest thinking is on the current hot topics - and isn't it interesting to be exposed to some quite extreme opinions, sometimes! Here's a list of some of the web logs I read, or at least dip into, to find out what's going on not just in biomedical editing but more widely.
High on my list is the COPE Council blog - http://publicationethics.org/blogs. Since October 2008, members of the Council of the Committee on Publication Ethics have been writing succinctly about matters of concern and interest to them (and us as ethically-aware editors). Recent topics include: Should all journals have one universal referencing style?; Concern about UK libel laws; When an editor knows that a submitted article omits to reference key works in the area, what should he or she do?
Ben Goldacre's series of "bad science" articles in the Guardian led me to his blog - http://www.badscience.net. At the time of writing, the latest post is about inaccurate science journalism: "There's nothing like science for giving that objective, white-coat flavoured legitimacy to your prejudices, so it must have been a great day for Telegraph readers when they came across the headline 'Women who dress provocatively more likely to be raped, claim scientists'. Ah, scientists. 'Women who drink alcohol, wear short skirts and are outgoing are more likely to be raped, claim scientists at the University of Leicester.' Well there you go. Oddly, though, the title of the press release for the same research was 'Promiscuous men more likely to rape'." Read the rest at http://www.badscience.net/2009/07/asking-for-it.
After all those years of working at BMJ, I hasten to mention its blog, http://blogs.bmj.com/bmj - which has a variety of writers from the journal and from the BMA writing on current biomedical concerns. The list of categories on the BMJ blog consists mostly of the names of regular writers, but also  includes some topics: carbon, conferences, credit crunch, digital media, flu pandemic updates, junior doctors, students, swine flu - and 245 posts by guest bloggers.
Nor is the BMJ the only journal with daily posts on topics of interest to its readers (often related to articles they have just published, or are about to - and why not?). Since the Wall Street Journal started in 1998 (blogs.wsj.com), every magazine and newspaper has hopped on  the bandwagon, and as journals have gone online, they've often found they "need" to add a blog. Keeping up with them all will keep you busy; I can list only a few from well-known international journals: www.biomedicaleditor.com/biomedical-editor-blog.html; http://blogs.sciencemag.org;  http://everyone.plos.org.
The best "one stop shop" must be http://blogs.nature.com. It's busy with "tracking blogs from nature.com and beyond. Find great science blogs, keep up to date with the latest buzz and read the latest posts from our editorial staff" - and yes, it does what it says on the tin, in the subject areas of Bioinformatics, Chemistry, Clinical Practice & Research, Earth & Environment, Life Sciences, Neuroscience, Physics, Science and Society. Some of the blogs it includes are Gobbledygook, Martin Fenner's blog on scientific publishing in the internet age (http://network.nature.com/people/mfenner/blog); Journalology: science publishing trends, ethics, peer review, and open access (http://journalology.blogspot.com/), 80beats "news aggregator, weaving together the choicest tidbits from the best articles covering the day's most compelling topics" (http://blogs.discovermagazine.com/80beats), and blogs for NPG authors (http://blogs.nature.com/nautilus) and peer reviewers (http://blogs.nature.com/peer-to-peer).
Blogs are available in many languages, and I hope readers will share their non-English favourites. Being educated in Canada, I'm not uncomfortable with reading French and am glad to know about the blog of ESE's former editor-in-chief, Hervé Maissoneuve. At http://redactionmedicale.typepad.com/redactionmedicale (also accessible as www.h2mw.eu) he writes punchy posts about current stories in the biomedical field.
The blogs of practising editors are often on their professional websites, and pass on grammar and style tips (for example, www.biomedicaleditor.com/biomedical-editor-blog.html) or generously give general writing and publishing advice (http://lillieammann.com/blog).
If you're new to the blogosphere, you'll find a plethora of blogs for any topic of interest. Apart from the writing and opinions of the writer, characteristics of the blogs themselves make some more pleasant than others . An uncluttered layout, and use of black text on a pale background (not vice versa) , make it easier to focus on the words, the argument. Visual material  can be important - those without photos can use the catchiness of the headline, and the words highlighted with clickable links. Categories and tags are useful for finding similar items in the archives; a list of related blogs is useful for "joining the community" - as reader or as blogger. We'd be interested to hear from EASE members involved in blogging on their journal's website: what's your experience?
 
Margaret Cooter
mcooter@bmj.com
(http://margaret-cooter.blogspot.com)
 
 
May 2009
 
EasyCalculation.com
   
I was once asked to calculate the geometric means for a large series of bacterial minimum inhibitory concentrations. Don't worry about what those are (for the purposes of this item), but the reality was that I was presented with 30 sets of data, each containing between 2 and 90 values. I did what every moderately sane editor would do - I panicked. Then I googled  "geometric" means (you can always rely on Google to help you out in a crisis), and one of the first sites listed was EasyCalculation.com. Serenity returned. I calculated my means using the idiot-proof tool provided, completed the table as required, and smugly sent it to my client. Another project was thus snatched from the jaws of disaster, and I suddenly had time on my hands. I started to look around the rest of the site.
   
  This is truly an Aladdin's Cave of math tools. It has dozens of free online calculators (no registration or downloading is required) where you can enter data and output parameters as diverse as the area of a square through negative binomial distribution, factorials, ideal gas law, basal metabolic rate, and even what size air conditioning unit you need for a room of a given size and aspect and what temperature you want to achieve.
 
In addition, there are detailed explanations of what each parameter is and what it is used for, thus enabling you to sound very knowledgeable when reporting in to the boss or the client - and learning plenty along the way.
 
If you have some "study time" to use then there is a bank of tutorials for you to work though. Although they require you to have basic mathematical knowledge, anyone who did secondary school maths should have no problem.
On the lighter side the site includes brain-teasers and some calculators intended to entertain rather than inform. My favourite fun page is imaginatively entitled "Funny Math", and here you can find all manner of little known mathematical facts. For example, who would know that 10 raised to the power 366 is called a Primo-Vigesimo-Centillion (and you might reasonably ask, "Why would anyone want to know?"). If you are interested in ancient number systems there is a wealth of information on those - did  you know, for instance, that the Babylonians' numbering system had only two basic elements  (| and <), meaning that anything bigger than three looks like a pyramid of martini glasses!
Take a look around this site, the property of HIOX in India, and I challenge you to not find something useful, of interest, or at least entertaining.
 
Moira Johnson-Vekony
europeanscienceediting@gmail.com

February 2009

Regular expressions
http://office.microsoft.com/en-us/help/HA010873051033.aspx
http://office.microsoft.com/en-us/help/HA010873041033.aspx
http://wiki.services.openoffice.org/wiki/Documentation/How_Tos/Regular_Expressions_in_Writer

One of the most powerful features of any text-editing package is its support for regular expressions. Using regular expressions as part of a find-and-replace operation enables you to make systematic edits to a document with remarkable speed.
Querying a search engine for something like "regular expressions" produces lots of helpful results, but in Microsoft Word and OpenOffice the syntax used for regular expressions, or regexes for short, is rather different.
Say one wanted to change "vapor" into "vapour", but only in those cases where it was a word on its own, not, for example, in "vaporous" or "evaporate". <(vapor)> (Word) and \<vapor\> (OOo) catch these cases, where the < and \< stand for the beginning of a word. Likewise, word-final "-ize" can be identified by (ize)> (Word) and ize\> (OOo). This, however, would be an unwise thing to do as it would also catch "size", "prize", "seize" and so forth. One can restrict the search to words longer than, say, six letters by writing [a-z]{3,}(ize)> (Word) and [a-z]{3,}(ize)\> (OOo), where the square brackets introduce a set of characters to be matched (this can be as simple as a single character, [n], or a range, [A-Z], or a mixture, [aeiou0-9]), and the braces indicate the number of characters to be matched, in this case at least three.
In general, the trickier the task being asked of the regular expression, the more similar the syntax in Word, OOo, and in programming languages such as Perl.
The above examples might seem somewhat contrived, but regular expressions come into their own for tasks such as rearranging formulaic subject matter such as addresses and bibliographies, and the Microsoft Word-specific pages are particularly focused on the tasks of rearranging names and dates. It's confusing that the full stop in Word regex syntax stands for a full stop, whereas in OOo it stands for any character, while in Word a question mark stands for any character and in OOo it means zero or one of the preceding character.
In short, regular expressions are so powerful that it is a very good idea to practise on test documents and compare the results carefully with the original before trying them out on a live piece. But they may well change your life.
As with many things, this has apparently changed in Word 2007 - but that is a matter for another column.

What is this file?
http://extensions.pndesign.cz/
RAR, SIT, CDR... A special case of three-letter abbreviations, and one that plagues technical editors, is the file extension. Authors are endlessly inventive at submitting files in peculiar formats, and the first question you need to answer is "What program did they use to generate that?" This page answers that quickly and neatly. The site is lightweight and simple to navigate.
I should note in passing that while Wikipedia is always something of a lottery, documenting the peculiar programs that can be used to open peculiar files is one of its strengths.
 
Abbreviations for editors
http://www.nactem.ac.uk/software/acromine/
 
  Anyone with experience of lists of abbreviations and acronyms will have spotted that they're seldom up to date and often contain abbreviations and acronyms which, from a cursory internet search, seem to exist only in lists, rather than out in the wild. So an abbreviation list that is somehow automatically generated from current material would be extremely welcome.
  AcroMine has been around for a few years but you may not have seen it before. The idea is to take all of PubMed and look for word sequences that regularly co-occur with expressions in brackets that match.
  But how well does it work across disciplines? My first attempt was a term used in nuclear magnetic resonance spectroscopy: INEPT. AcroMine correctly identifies this as "insensitive nuclei enhanced by polarization transfer". AcroMine offers 22 hits for "MMR"; the most common is, surprisingly, not the vaccine against measles, mumps, and rubella but "mismatch repair". AcroMine even correctly offers "Large Hadron Collider" as an expansion for "LHC", demonstrating that these days PubMed is a resource for scientific, technical, and medical editors of all disciplines.
 
  Online biochemical and chemical nomenclature
  http://www.chem.qmul.ac.uk/iupac/
  This website may look old-fashioned, but it will still be invaluable when the likes of Facebook are a distant memory. Here on a single page are many of the recommendations of the International Union of Biochemistry and Molecular Biology (IUBMB) and those recommendations of the International Union of Pure and Applied Chemistry (IUPAC) that are particularly relevant to editors working in the life sciences.
 
Blog update
http://scienceblogs.com/notrocketscience/
http://www.badscience.net/
http://david-crystal.blogspot.com/
 
Many journal publishers (BMJ, OUP, NPG, RSC, ACS) are using blogging to promote their own articles, but I thought it would be more interesting to look at some contrasting blogs from the very different worlds of science and medicine.
Ed Yong's Not Exactly Rocket Science concentrates on readable accounts for non-experts of peer-reviewed published material. Readers outside the UK might be unfamiliar with Ben Goldacre's Bad Science, which is both a column in The Guardian and a rather longer and more-often updated blog covering how the media reports medicine. It is a sobering but immensely entertaining read.
Lastly and most relevantly for people whose job is working with language, David Crystal, scourge of prescriptivists, has a blog about how language actually works which is well worth following and learning from. An excellent comment on style guides is worth repeating in full:
Style guides should be explaining to people what English allows us to say and write, and pointing out the strengths and weaknesses of different usages in different contexts. Blanket bans are a nonsense.
 
Physics and physical chemistry
http://old.iupac.org/publications/books/gbook/
 
The International Union of Pure and Applied Physics (IUPAP) doesn't put its recommendations online, but IUPAC's Green Book, which is based in part on the recommendations of IUPAP and also on ISO 31 (now superseded by ISO 80000-3:2006, which costs only CHF 96), is online as a PDF of its second edition, and the third edition will appear online soon.
It's an indispensable vade mecum for editing equations and the kind of mathematical expressions that one sees in running scientific text and was immensely useful throughout my doctorate and my years as a technical editor.
 
 
Colin Batchelor
batchelorc@rsc.org
 
Thanks to Richard Hurley