ACRL 2013 Poster

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My colleague Eileen and I presented a poster entitled Research Paper Planner:  Students Love It, but Do We Know Why? at ACRL on Friday, April 12, 2013, 2:30-3:30 pm.

Here’s a link to the pdf of the poster (ACRL2013Poster).  Just to warn you, the file is over 6M.

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Using Fedora and OAIS

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As I mentioned last time, for one of my classes in library school, I am learning about digital curation. We’ve been learning both about the theories and models behind digital curation in addition to getting some hands-on practice with some of the computer programs and tools used in digital curation. So the question arises, how do the theory and practice mesh?

One of the theoretical frameworks used in digital curation is the OAIS (Open Archival Information System) model. One of the most important aspects of this framework is to give names and definitions for different objects, roles, and function in digital curation. Specifically it defines and describes data as submission information packets (SIPs), archival information packets (AIPs), and dissemination information packets (DIPs). The model also includes a “flow chart” of functions depicted below which shows how SIPs that producers generate transform into AIPs which are curated by mangement and eventually into DIPs which are used by consumers. Each of these transformation requires metadata to describe the data. The model does not prescribe any particular software or methods for data ingestion, preservation planning, data management, archival storage, access, or administration.

Because OAIS does not prescribe any particular method for data curation, any number of tools and software can be used. The group I’ve been working with for the past few weeks used a repository software system called Fedora. Fedora is open access software which means you don’t have to pay for it and you can customize it to your needs. The system we played was pretty barebones and had both a graphical user interface (GUI) that you can access from the web and a command line interface (CLI) that you can access from the unix server where the software was installed.

One thing that I enjoyed doing was matching up the GUI commands with the CLI commands: so clicking on the “Add” button in the GUI simply asks for all the inputs for the CLI fedora_ingest command and executes it. The GUI commands were pretty self-explanatory because the system would simply ask you for all the inputs it needed although it would have been nice if there were a few more explanations. I also found the location of some action tabs not logical. The CLI commands were harder to figure out because the documentation is very terse and I wasn’t always sure what all the terms meant. It also would have helped if the documentation had more examples.

From the GUI interface, it was pretty easy to upload files from my harddrive, to display files, and to modify the information about them. I would have liked the ability to move files or folders around. I didn’t try uploading or downloading files from the CLI interface because it was a pain to move the files to/from my harddrive from/to the server. One thing I noticed was that the files that are generated when data are uploaded are not all located together. I never quite figured out the rhyme or reason of how the information was stored so there would be no simple way to move files around.

Now, back to the original intent of this post, how does theory play out in practice? I would say that it is pretty easy to distinguish the SIPs, the AIPs, and the DIPs from each other. The SIPs are the uploaded files, and the DIPs are downloaded files so the functions of ingest and access are self-explanatory. The AIPs are stored on the server and Fedora adds metadata to describe the data so the process of archival storage is also in Fedora. Commands for data management I found a bit lacking: you can edit metadata and purge or erase files but you can’t move the files. Preservation planning and administration in OAIS are bigger picture functions and don’t involve working with individual files in the repository. So, overall Fedora fits the data curation scheme put forth by OAIS.

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Data Curation Intro

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Wordle: Digital Curation As I have mentioned before I am currently taking classes for my library degree.  As part of my degree I am planning on getting a certificate in digital curation. What exactly is digital curation and why am I interested in it?  I’m actually interested in digital curation as a part of data management/curation.

Most people associate libraries with books, but probably more accurately libraries should be associated with information (which is often found in books, but also in journals, maps, pictures, electronic resources, and other formats).  Data or facts are not very useful or informative until put into some sort of context.  Part of this context includes the description of the content of the data and where it is stored.  In other words, data about the data, or what librarians call metadata, helps data become information (or something useful).

Although everybody has data (think about your photographs and other “collections” around your house), I want to help researchers (specifically those at Baylor) transform the data they collect or generate into information that the world can find and learn from and even use for further research.  I see this process of transforming data into information as curation (although I often wonder if curation is a word since it always is underlined as being misspelled).

To me this process of curation means first working with researchers as the generate or collect the data to make sure the data is described well and stored properly.  Then helping them decide which data should be kept (raw data or reduced data, for example) and who should have access to it.  For the data that are kept, the next step is making sure that they are stored somewhere permanently and accessible to others who might want to view and perhaps reuse them and not just on a random harddrive somewhere and making sure that there is a plan to review and update the data and upgrade the storage over time.

The hard part I anticipate is getting researchers to include these curation steps as part of their workflow.  Although mandates from funding agencies have begun to nudge researchers into thinking about data curation, I don’t think that researchers will really buy into the idea and change their habits until they see some sort of benefit to themselves.

How data curation will be incorporated into a researcher’s workflow is largely dependent on discipline and the type of data.  Even though they may all be biologists, a researcher who runs clinical trials will have very different types of data than one who analyzes genome sequences or one who tracks endangered species in the field.  Nevertheless, much of the data collected and generated today in the sciences and social sciences and increasingly in the humanities is digital (hence my pursuit of a certificate in digital curation).

In my courses, I’ll be learning about different about software that can be used to manage digital data.  The different programs seem to be strong in different areas:  description, organization, discovery, storage, preservation, etc.  I’m not sure how much I will use any of these programs regularly as the STEM librarian at Baylor, but it will be important for me to know them as I try to guide researchers and the university into turning their data into information.

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2nd Texas STEM Librarians Conference

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Last Thursday to Saturday, I had the pleasure of attending the 2nd annual STEM librarians conference in Denton.  The conference almost doubled in size from last year and UNT did a great job of hosting.

Discovery Park Library Service Desk. We met in a computer classroom behind this area

Librarians from all around Texas (but mainly the DFW area) presented on all different subjects even though the theme for the conference was e-books.  In addition, there were roundtable groups and panel discussions with various vendors.

The pre-conference on Thursday was on gaming and education.  We spent the afternoon playing educational games from this list and heard an interesting talk about from an educational psychologist on gaming and learning.  For a bit more fun, another librarian talked about her library’s role in a game of Humans vs. Zombies on her their campus.  She even has a research guide on how to survive a zombie attack where she has also posted her presentation.

Friday was a mix of discussions, lightening talks and regular presentations.  Some of the talks were more technical talks geared towards librarians, but some of them talked about resources that we should make available to our patrons such as a guide for K-12 STEM resources, databases on toxicology, hazardous chemicals, environmental health, and toxic releases, and a video journal which I will talk about more next week.  We also talked about open-access publishing and data management/curation which are issues that concern both STEM researchers and librarians.

The Saturday post-conference session was focused on e-books.  I cobbled together a presentation based on my two posts on downloading library e-books.  A talk about how one library did an analysis of their e-book purchasing in proportion to their collection development budget really appealed to the analytical side of me but would probably bore most of the readers of this blog.

Overall, a very enjoyable two days of conferencing.  It was a small but focused conference which made the introvert side of me very happy, and I was able to make some new contacts and renew some old contacts which will be very helpful when it comes to my 4th year review next fall.  But most importantly, I learned a lot of things that will help me be a better science librarian and serve you better.

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User-Centered Spaces

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As some of you may realize, in addition to working as the science librarian at Baylor, I’m taking classes towards my library degree.  We’ve been discussing innovative or renovated STEM libraries.  I am particularly interested in the Applied and Engineering Technology (AET) Library at the University of Texas San Antonio (UTSA).  I’m interested in this library because I am thinking about how the libraries at Baylor can have a presence in the Baylor Research and Innovation Collaborative (BRIC).  I’m hoping to use information from the UTSA library websites, newspaper articles, what I remember from a tour during Summer 2011, and an IM chat with someone from the UTSA library as the basis for my discussion.

After a soft opening in June 2010, the AET library had its grand opening in Fall 2010 in converted labspace the Applied and Engineering Technology Building.  The most notable feature about the library is that it is bookless.  It is this aspect of the library that prompted an article about the library in Inside Higher Ed which was then picked up by both USA Today and the New York Times.

The emphasis of this library is to provide spaces that students will use.  Two large group study rooms seat six people and have 42″ LCD monitors and whiteboard and glass walls that students can write on.  A smaller study room seats four people and also has whiteboard and glass walls.  All study rooms can be reserved in advance and are available on a first-come basis if not reserved.  In addition to numerous personal study spaces for students with laptops are 10 public computers, a scanner, and a color printer.  White boards for individual use are also available throughout the library.

But a bookless library is not devoid of information.  The AET library has a reference desk that is staffed while the library is open by STEM student assistants who answer basic reference questions and refer more complex questions to either the science or engineering librarian.  These librarians also spend time in the library helping students.  In addition, all of the online journals, databases, and e-books available through UTSA libraries are also available at the AET libary.  The AET library even has a pilot e-reader program where 2 Kindles, 2 Sony e-readers, and 1 Nook which are pre-loaded with a number of STEM books.  Students can request that a book be bought and downloaded to the e-readers (although this has happened only once).

Because the AET libary is user focused, the librarians have made a number of changes even in the short time the library have been open.  Most of these changes are to encourage group work among students.  They have added stools to take advantage of the old lab benches that were original to the building; they decreased the number of overstuffed chairs that had very small attached desks; and they added more tables and white boards.

The AET library is an excellent example of a library that has made the most of the space they were given to serve users.  I would love to set up a similar space at Baylor in our new BRIC facility.

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How to Deal with Rejection

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Mug from the Journal of Universal Rejection

So after last week, you’ve picked what journal to submit to, and you wait (and wait and wait) to see whether your paper is accepted.  When the day finally comes, your paper hasn’t been accepted.  And if you’re like me, you get filled with a range of emotion to the point of crying.

But as was pointed out to me recently in an email from the National Center for Faculty Development and Diversity, we should think of rejection rates like batting averages.  A batting average of .4000 is almost unheard of.  And a batting average of .2500 is pretty good.  So if one out of every four submissions is accepted, you’re doing pretty well.

So, after about a week when the sting of the rejection is not quite strong, I would suggest reading thoroughly through the reviews.  The associate editor should have given his/her own opinion along with a summary of the strongest points from the other reviewers.  Analyze these reviews.  They should give you good feedback.  In fact, for scholars who have moved on from having an adviser, they often look at the feedback from reviewers as the type of feedback they would have received from their adviser.

If the reviews don’t have any major corrections in terms of methodology, analysis, organization, or conclusions but just don’t seem that excited about the results, you’re in luck.  You may have simply targeted the wrong journal in terms of audience so make the minor corrections and submit the article as soon as you can (within a week or two) to another journal that might be more interested in  your topic.

If the reviews ask for more substantial changes in terms of methodology, analysis, organization, or conclusions, you need to determine which of these suggestions is feasible in a reasonable amount of time (one or maybe two months).  Sometimes you can’t rerun an experiment or go back into the field, sometimes you can.  More than likely you probably just need to explain more explicitly your reasoning of why you did what you did or acknowledge the limitations of your study.  Often we are so familiar with our work that steps become obvious to us that are not obvious to people outside our lab, or reviewers (especially those who are on the periphery of our research specialty) take a leap to a conclusion that we did not intend them to take.  Try to make these revisions as soon as you can and resubmit to either the same journal with a cover letter saying how you have addressed the previous reviews or to a different journal.

Some people suggest resubmitting papers as is even if more substantial changes have been requested.  I personally don’t think this is the best idea.  Keep in mind that even if you submit to another journal, you might end up with the same associate editor or reviewers, and they get annoyed if they have to review a paper again that they didn’t like the first time.  I’ve actually had two or three people complain to me about this recently.

In very, very special circumstances, you might wish to appeal the decision or ask for new reviewers; but in general, you are probably better off submitting to a different journal.  If a paper has been rejected three times after revisions, you might want to consider working on a different project or with some different data.

But the main point of this blog:  resubmit, resubmit, resubmit!

The information for this blog comes partly from my own experience but mainly from these three posts from Tomorrow’s Professor#197 How do you handle rejection, #754 On journal rejection, and #939 Responding to journal decisions.

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Where to Submit an Article

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Since we seem to be talking about scientific writing this month, the question of where to submit your article arises.  Now the easiest thing to do is to look through the list of references you used and see which journal(s) you cited the most often, and then submit to that journal.  You can also ask your colleagues or adviser who have read the paper for suggestions.

But if you’ve narrowed the list down to two or three journals, how do you decide which is best?  There are two things to consider:  relevance and accessibility.

By narrowing down your list to journals that you have cited is the first step in addressing relevance.  But you also have to decide whether you submit to a general journal in your area (like Journal of the American Chemical Society or Acta Mathematica or Biological Bulletin or Geological Society of American Bulletin) or one that addresses a specific field (like Organometallics or Technometrics or Clinical Genetics or Tectonophysics).  There is also the option of submitting to a general science journal like Nature, Science, or the Philosophical Transactions of the Royal Society of London.

In order to be relevant, the significance of your results needs to match the significance of the journal.  In other words, would scientists outside your discipline (i.e. geologist if you are a biologist or a mathematician if you’re an engineer) be interested in your results?  If so, submit to a general science journal.  Or would other scholars in your discipline be interested in your results (i.e. the grad students in the lab two floors down)?  If so, then submit submit to a general discipline journal.  If only people in your lab (and maybe the lab next door) would be interested in your results, then submit to a subject specific discipline journal.

But not all general or even subject-specific journals are equal.  In order to be accessible people need to be able to find your article and be able to read it once they find it.  You want to maximize the exposure of your article or make sure that it is discoverable.  Since most people use index databases to find articles, you want to make sure that the journal you submit to is indexed in all the databases relevant to your field.  Ulrich’s Web is a good place to find that information.  Just look for the journal in question and then scroll down to the Abstracting & Indexing section.

Open access journal let are available to anybody to read.  You might want to consider submitting to one of these to up the accessibility of your journal, but remember that these journals come with high (and sometimes) prohibitive page charges.  Libraries and individuals are more likely to subscribe to high impact-factor journals so you might want to check the impact factor of the journal you’re interested in.  Remember to compare it to other similar journals and not rely on an absolute value.  Other considerations such as average review time, high subscription costs, or boycotts might play into your decision.

So the key is figure out the journal that would have the biggest interested audience in your work.

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Scientific Jargon

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Following up on last week‘s post on the book Scientific English by Day and Sakaduski which has some useful lists of “Problem Words and Expressions” and “Words and Expressions to Avoid,” this week I present a list of terms that have different meanings to scientists and to the general public.  I was first alerted to this list on a blog by the Eric Berger, science writer at the Houston Chronicle.

This list originally came from an article in Physics Today which discussed how climate scientists can improve how the present their findings to a general audience (hence, the inclusion of aerosol).  I would add to the list negative trend and negative feedback.  Every field has its set of jargon or terms that have different meanings in that field (one notorious example in geology is cleavage).

I’ve been a scientist long enough (and maybe you have too) so that I know exactly what all these terms mean and use them correctly without thinking about it.  But at times when I’m talking to my colleagues (most of whom are humanists which is not unusual among librarians) or to students, I get funny looks and I realize that I’ve used a term that doesn’t make sense to them.  What I worry about are the times when I don’t get the funny look and what I’ve said gets interpreted wrong.

My point here is not to avoid using these terms.  They are very appropriate to use when writing scientific papers and articles, but to be aware when you use them among the general public.  It is also a good list for beginning scientists to familiarize themselves with so that when they encounter them in journal articles they can interpret them correctly.

What are some words in your field (jargon) that have different meanings in common use?

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Book Review: Scientific English

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On occasion I plan to review books on the blog.  Some will be of professional interest; others will be of general science interest.  I doubt if too many of them will be for fun (unless I find a really good mystery novel set in a science department of a university).  Today I will review Scientific Writing by Robert Day and Nancy Sakaduski.

I was first introduced to this book by the writing center at my last institution.  We called it the dancing pencil book because that was what was on the cover of the second edition. As you can see, the cover on the third edition is much more subdued.

I recently purchased for Baylor a multi-user e-book version of the latest edition.  This means more than one person can look at or download the e-book at one time.  And I highly encourage you to read this book.

The book is easy to read.  I finished it an afternoon.  The text is sprinkled with good examples, pithy quotes, and cartoons.  All of these make the book entertaining and might even elicit a laugh or two.

What I like about the book is Day’s emphasis on clarity and logic.  He believes that there is an inherent beauty in science so that the writing does not need to be embellished.  Clear and simple writing brings out the beautiful science.  He also believes that if one learns how to think logically then one can write logically.  Grammatical syntax will fall out naturally if the writer thinks logically.

Day also emphasizes that there is a difference between literary writing and scientific writing.  He acknowledges that most readers of scientific writing are not native-English speaking Ph.D’s but rather students and international scholars.  As a result, he encourages parallelism and and discourages redundancy so that scientific writing is easier to understand.  He tells writers to be specific and not vague and teaches them how to use proper transitions between thoughts and paragraphs.

If you had an English teacher in middle school that you thought was too hard and boring, you will probably recognize that this book is essentially a grammar book.  It covers parts of speech, phrases, clauses, sentences, paragraphs, and punctuation.  Because the book is targeted to scientists, there are sections that discuss scientific nomenclature, abbreviations, and jargon. Scientific Writing does not simply define these terms but shows how these different words and structures can be used effectively (and sometimes ineffectively).  Sometimes, the counterexamples are more effective at demonstrating a principle than the examples.  The appendix on problem words and expressions is especially helpful.  New to this edition is a chapter that address writing for electronic media.

Yes, I know you will groan because I am recommending a grammar book to you to read.  But my students in the past were pleasantly surprised when they read this book and found it extremely helpful.  (And it has made me hyperaware of how I am writing this post.)  Look through it and tell me what you think.

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Reading Library E-Books

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So, finally after last week‘s e-book explanation, this week we will actually read library e-books on the Nook (I feel I should give the Nook a name).  We will download books from OverDrive, EbscoBooks, and Ebrary.  After trying, I am happy that I got a Nook instead of a Kindle because a Nook can read many more e-books especially those that have DRM.

I started by downloading Adobe Digital Editions on both my work PC and my home Mac. This is a fairly simple process but does require registering a username with Adobe and authorizing each computer to access the account.  Even though both computers are authorized to the same account, the downloads are not kept on the cloud so what is downloaded on my work PC is not the same as what is downloaded on my home Mac.Since I’m at Baylor, the public library I use is the Waco-McLennan County Library.  From the homepage, to get to the e-books click on the Download Books and Media link and then the Download Audio and Ebooks link which will take you to the OverDrive page associated with this library.  The first time I made the mistake of trying to find e-books through the main catalog. Browse through the books.  Add up to 5 to your cart.  Check them out.  Download them.  You will have to have your library card and pin (I had to call them to get my pin number) to check out the books. If you need to redownload the books, you can do so under My Digital Media Account.

For EbscoBooks, the process is fairly similar.  You need to have an Ebsco account (equivalent of a library card) which uses an email and a password.  Search or browse for a book, and then click the download link.  You have the option of searching for only downloadable books.  Currently, 7 days is your only option for borrowing a book.  If you need to redownload a book, the books are listed under My Checkouts.

Like for EbscoBooks, you need an Ebrary account to download books.  In this case, you need to create a username and it can’t be an email address.  Most Ebrary books allow you to download a pdf of (or print) 60 pages at a time with no DRM.  However, there are a limited number of titles (I haven’t figured out how to find them yet and I think it has to with the library’s Ebrary settings) that allow downloads of the full book to Adobe Digital Edition.  After you search or browse the books, click on the download link.  Then simply pick whether you want the partial or complete download.  If the full download is not available, it will tell you.  I haven’t found a way to see which books you have checked out since they are not automatically listed in a folder or on a bookshelf.

On the PC using Firefox, the files were downloaded into a folder called “My Digital Editions” and opened up automatically in Adobe Digital Editions.  On the Mac, Safari downloaded the file onto my desktop (the default).  I then moved it to the “My Digital Editions” folder and then double-clicked on the .acsm file to open it.

One nice thing is that each book in Adobe Digital Editions has a banner on it letting you know when the book will be due.  You can also return the book to the library if you finish reading it before the due date.  I’m not sure what happens to the book when the due date is reached since I haven’t had any of my books out that long yet.

To transfer the books to the Nook, simply connect the Nook to the computer with the USB cable.  Then open up Adobe Digital Editions.  Under the standard bookshelves will be one labelled Nook.  Simply drag the books you want to the Nook bookshelf and the files will be synced.  Make sure you have enough room for the books you want to read.

Everything I downloaded seemed to work well although I do prefer reading ePubs on the Nook to pdfs.

Posted in All Scholars, Books, Reading, Websites | 1 Comment