Archive for September, 2006
Welcome! Hello Petermr, and welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Here are a few good links for newcomers:I already knew how to edit Wikis but even if you get it wrong someone will tidy it up. The main thing that worried me was whether I would be able to fulfil the high standards. So I read the five pillars and they are worth reproducing in full:
I hope you enjoy editing here and being a Wikipedian! Please sign your name on talk pages using four tildes (~~~~); this will automatically produce your name and the date. If you have any questions, check out Wikipedia:Where to ask a question or ask me on my talk page. Again, welcome! – UtherSRG (talk) 13:02, 5 December 2005 (UTC)
- The five pillars of Wikipedia
- How to edit a page
- Help pages
- How to write a great article
- Manual of Style
Wikipedia is an encyclopedia incorporating elements of general encyclopedias, specialized encyclopedias, and almanacs.Wikipedia is not an indiscriminate collection of information. It is not a trivia collection, a soapbox, a vanity publisher, an experiment in anarchy or democracy, or a web directory. Nor is Wikipedia a collection of source documents, a dictionary, or a newspaper, for these kinds of content should be contributed to the sister projects, Wikisource, Wiktionary, and Wikinews, respectively.Wikipedia is not the place to insert your own opinions, experiences, or arguments — all editors must follow our no original research policy and strive for accuracy. Wikipedia has a neutral point of view, which means we strive for articles that advocate no single point of view. Sometimes this requires representing multiple points of view; presenting each point of view accurately; providing context for any given point of view, so that readers understand whose view the point represents; and presenting no one point of view as “the truth” or “the best view”. It means citing verifiable, authoritative sources whenever possible, especially on controversial topics. When a conflict arises as to which version is the most neutral, declare a cool-down period and tag the article as disputed; hammer out details on the talk page and follow dispute resolution. Wikipedia is free content that anyone may edit. All text is available under the GNU Free Documentation License (GFDL) and may be distributed or linked accordingly. Recognize that articles can be changed by anyone and no individual controls any specific article; therefore, any writing you contribute can be mercilessly edited and redistributed at will by the community. Do not submit copyright infringements or works licensed in a way incompatible with the GFDL. Wikipedia has a code of conduct: Respect your fellow Wikipedians even when you may not agree with them. Be civil. Avoid making personal attacks or sweeping generalizations. Stay cool when the editing gets hot; avoid lame edit wars by following the three-revert rule; remember that there are 1,408,046 articles on the English Wikipedia to work on and discuss. Act in good faith by never disrupting Wikipedia to illustrate a point, and assume good faith on the part of others. Be open, welcoming, and inclusive. Wikipedia does not have firm rules besides the five general principles elucidated here. Be bold in editing, moving, and modifying articles, because the joy of editing is that although it should be aimed for, perfection isn’t required. And don’t worry about messing up. All prior versions of articles are kept, so there is no way that you can accidentally damage Wikipedia or irretrievably destroy content. But remember — whatever you write here will be preserved for posterity.So how do these rules relate to creating an “Open Data” entry? First we should ask whether it is necessary. Frequently we see duplicate entries in WP that zealous editors spot and suggest should be merged or otherwise tidied. For example, OD might be seen as part of Open Access. I don’t believe it is and will defend this view with reasoned arguments and historical references. Secondly we must strive for Neutral Point of View. That means that I and others must not use it to promote OD although we can reasonably list some of our writings if they are substantive to the entry. The entry is not “mine” but “ours”. It would be completely appropriate to collect evidence that there was opposition to Open Data. But the page is NOT a debate between two sides, howerve carefully reasoned, although it could record such debates if they were deemed to be sufficiently important. Soon we’ll create an entry and follow its progress… P.
This means that any use of “Open” is likely to be fuzzy and confusing. The “Open Access” movement is broad and supports several major points of view which, though overlapping, have significant differences either in pragmatics or philosophy. Moreover “Open Foo” does not imply “Open Bar”. Thus “Open Access” publications will not by themselves ensure “Open Data”. More on this later…
- Open-source software, software which permits the use and modification of its source code
- Open source hardware, or open hardware, computer hardware, such as microprocessors, that is designed in the same fashion as open source software.
- Open source record label, open source music
- Open content, another term for open source, when the distinction between source and product is less clear
- Open Source Car, open designs for next generation vehicles.
- Open Source Definition, as used by the Open Source Initiative.
- Open-source license, a copyright license that makes the source code available with a product.
Society and culture
- Open-source advocacy
- Open source culture
- Open source ethics
- Open-source evangelist, is a person who promotes open-source software.
- Open source funding
- Open source government, open source in government
- Open-source unionism, an innovative model for labor union organization.
- Open source movement, a movement that advocates open source software.
- Open source development model
- Open source politics, a political process that uses Internet technologies to provide a rapid feedack mechanism between political organizations and their supporters.
- Open source governance, application of the philosophies of the open source movement to democratic principles, e.g. to enable any interested citizen to add to the creation of new policy.
- Open Source Committee
- Open source journalism
OrganisationsOpen-source software related:
- Open Source Initiative, an organization dedicated to promote open source.
- Open Source Development Labs (OSDL), a non-profit corporation that provides space for open-source project.
- Open Source Technology group, news, forums, and other resources for IT
A good deal of the reasoning behind transcription of spectral data in publication is to impart meaning to the spectra. The 1H NMR spectrum of rasfonin, for instance, would be indeciferable to me, but the data written in the publication, transribed by the author and annoted for every peak would make (more) sense. It’s great to get an idea what the spectra look like, but more often than not, the actual spectra can be found in the supplementory data as a scan of the original. The combination of these two data sources gives the synthetic chemist everything they need.Before I get onto the horror, Let me make it very clear that Tot. Syn’s blog is excellent and I’m hoping that he can meet us at the Pub on Monday lunch. His blog is a model of the future of chemoniformatics and we’d like to bounce some ideas off him. (I’m also not specifically criticising the authors of the paper – at least not more than all other organic chemists because this supporting information (SI) is typical. I am of course suggesting gently that the process of publishing organic chemical experiments is seriously and universally broken). The supporting information is a hamburger PDF and this example excellently makes my point. (Please readers, read it – or as much as you can manage – as I need help. Especially from anyone who is involved in graphical communication). It’s a separate document from the original paper and even though on the ACS site remarkably seems to be openly viewable. Maybe the ACS will close it sometime or maybe this exercise shows that Openness enhances downloads. The SI draws the spectra on their sides! This is a clear indication that they aren’t meant to be read on the screen, but printed out. But the SI is 106 pages long. That’s not unusual – we have seen over 200 pages. I am sure that many organic chemists who want to read it will print it out rather than trying to read it on the screen. The spectra run from pp 36-107 with no navigational aids – if you want to link a compound to its spectrum you have to scroll through the spectra till you find its formula. Some compounds are depicted as chemical formulae on the spectra and some, but not all, contain index numbers (bold in the text). Let’s assume that you are at a terminal and your lab has used up its paper bill. You scroll down to the infrared spectrum of a compound: It doesn’t look very promising, so I turn my head 90 degrees to look at it. Not very comfortable. So there is a tool on Adobe reader that rotates the page to give: This is awful. It looks like the spectra I used to collect 30 years ago when the pen plotter was running out (before that we plotted the spectra by hand it’s good for the soul). The resolution is probably 0.1 or better in the x-direction. I have no idea why it is so awful. Now we want to look back to the text where the author has made the annotations (there are no annotations on the spectra so we have to skip back 70 pages) to find: Our helpful Adobe reader has turnd all the pages round, so we have to turn this one back again. And, I suspect, the only real way to navigate this is to print it out. The authors obviously spent a lot of time preparing this SI. The publisher probably calls it a “creative work” – you can claim copyright on creative works. I’d call it a destructive work. It doesn’t actually have a copyright notice, although the ACS has a meta-copyright where they assert copyright over all SI (except one from Henry Rzepa and me). Now – please help me with the PDF. I have blogged earlier about OSCAR - the data extraction tool that can extract massive information from chemical papers in HTML or even Word. But it doesn’t work with PDF. Is there any way of extracting all the characters from this document? If I try to cut and paste I can only get one page at a time? Yes, I could probably hack something like PDFBox. But otherwise PDF is an appalling efficiently way of locking up and therefore destroying information. The message is simple: STOP USING PDF FOR SCIENTIFIC INFORMATION DO NOT USE PDF FOR DIGITAL CURATION
to research the development of digital repositories. Three groups have been collaborating in chemistry, with a strong emphasis on crystallography and spectroscopy. This involves all aspects – building software, designing metadata specs, and understanding the way chemists work and think. We have found that the social aspects are at least as important as the technical – I won’t eleborate here yet as these will be reported at:
The Trust provides additional funding to cover the costs relating to article-processing charges levied by publishers who support this model. • Approximately 1% of the research grant budget would cover costs of open access publishing
In that case, perhaps you should have parted with the observation “ACS is a problem”. , but partly serious.I thnk the tone of this is out of keeping with this blog and I am therefore writing a “moderatorial”. This was a term I used (I doubt it was a neologism) when Henry and I ran the XML-DEV list. A Moderatorial (example) was to guide the list, but not constrain it. Although this is not a list, anyone can post a comment and I will automatically post it whether or not I agree with the sentiment. However I wish to avoid flame wars and ad hominem remarks and outline my own philosophy on this blog. I try to post statements which are accurate and not unnecessarily emotive. I do not completely have a strict Wikipedian-like Neutral Point of View (NPOV) in my posts and use the list for advocacy. However I do not wish the comments to be one-sided and invite a range of views – the result might indeed be neutral. I take as an example the excellent blog from Peter Suber – he is analytical and incisive. A typical example read:
This is a style I strive to emulate. PeterS has a position of advocacy (Open Access through various models) but reports accurately and without ad hominem arguments. In the present case it is clear that the devil is in the details. Whether I welcome or criticize the ACS hybrid policy depends on whether it enhances the free use of data. It sounds dubious from PeterS’s report, but hopefully there will be more clarity from all parties. In the case of control of published data – my fundamental position is that scientific data belongs to the commons and that there is good legal and moral precedent for this. The stronger this basis, the stronger the case. Open Access is complex and, I believe, changing so that entrenched positions are not always helpful. Although I wish for total Open Access I am prepared to work with publishers operating different models. My engagement is dedicated to trying to make scientific data Open. I have frequently been asked to speak at the ACS meetings and have accepted. My advocacy for Open Data is robust but hopefully not personal. People and organisations are flexible. Thus, for example, I gave a talk at ACS last year in the Open Access session. There were presentations for and against Open Access and (in my opinion) the Open ones were better presented and more compelling. But I still listened carefully to all arguments. My own presentation was a demonstration of the power of data and the value of Opening it. As a result Pieter Borman invited me to talk at the annual meeting of the STM publishers in Frankfurt. I went with some doubt as to whether my arguments would be taken on board – but I had a good audience – and I heard (though I can’t find details) that STM publishers have recommended that scientific data should be copyright free (confirmation is welcomed). So I don’t take entrenched positions about people and organisations, but about issues. The Firefox/downloading episode is a problem – I have highlighted it – and hope that the factual analysis makes a useful contribution. It might not change policy directly but it should help to avoid misunderstandings. Finally therefore I shall directly accept all non-spam comments, but reserve the right to issue moderatorials if I feel the comments might ignite flames. P.(From ACS press release)In October, American Chemical Society journal authors will have the option of paying to immediately provide free online access to their articles on the society’s website. Authors will also be able to post electronic copies of their sponsored articles on personal websites and institutional repositories. Fees for the program will range from $1,000 to $3,000 per paper, depending on whether the author is an ACS member or is affiliated with an institution that subscribes to ACS journals.Comments (from PeterS). (2) See my (PeterS) nine questions for hybrid journal programs, just published on Sunday. Of the nine, the ACS announcements give good and welcome answers to two: it will let authors deposit articles in repositories independent of ACS and it will not retreat on its green self-archiving policy. It gives unwelcome answers to two more: it will not let participating authors retain copyright and it does not promise to reduce its subscription prices in proportion to author uptake. (Hence, it plans to use the “double charge” business model.) It leaves us uncertain on the remainder: Will it let participating authors use OA-friendly licenses? Will it waive fees in cases of economic hardship? Will it force authors to pay the fee if they want to comply with a prior funding contract mandating deposit in an OA repository? Will it lay page charges on top of the new AuthorChoice fee? (3) The ACS has been a bitter opponent of OA through PubChem and FRPAA. But I don’t believe it ever opposed the very idea of charging author-side fees to support the costs of a peer-reviewed journal, as some other hybrid journal publishers did before adopting the hybrid model.