Zotero 2.0 and archaeology

Bibliographic software are an essential part of the software suite of many researchers, providing an important means of organising citation data and associated documents and notes. In recent years, this software also become increasingly good at allowing researchers to directly import new references found on the web into their reference collections at the click of a few buttons. However, the recent release of a fairly stable Beta version of Zotero (2.0) – an open source bibliographic software – suggests that bibliographic management may soon be turned on its head.

JSTOR: Oceanic Linguistics, Vol. 3, No. 2 (Winter, 1964), pp. 248-265Zotero is an extension, or plugin, for the free web browser Firefox and has been around for a while; indeed, I have written about it before and I’m still an enthusiastic advocate. The application sits inconspicuously in the bottom of of your web browser and allows you to directly import references from a very wide range of sources including journal databases, search engines such as Google Scholar, or library catalogs. Once in your reference collection, you use the program as your bibliographic manager, placing items into categories, attaching research notes and so on. The people at Zotero have a very good range of introductory tutorials, so I won’t cover that here. Overall though, it’s quite a nifty little program; for example, it can download whole pages of references from Google scholar or journal databases as well as import from or export to other bibliographic software packages. You can also use Zotero to cite references and compile reference lists in documents that you are working in both Microsoft Word and OpenOffice.

One reason I think Zotero 2.0 will change the way many academics use bibliographic software is that it has various tools to enable collaboration across the web. Whereas Zotero 1.0 sat in your browser enabling you to acquire and manage your references, 2.0 enables you to:

  • Synchronise and backup your Library to the web or another computer;
  • Create public or private ‘groups’ on the web, allowing group members to collectively build reference collections online;
  • search public collections compiled by other researchers;
  • seemlessly add references found in public collections to your own collection

This will be of great value for teams working on collaborative research projects because it will allow team members to work from and also contribute to a central reference collection on the web.  It may turn out to be a useful tool in various contexts, including:

  • university lecturers or teachers seeking a single, web-friendly reference collection on a particular subject or topic;
  • publishers, societies or organisations wanting to improve accessibility to their publications;
  • researchers who want to compile a list of their own publications on the web, as a supplement to online resumes and so on;
  • collaborators working on research projects involving multiple individual researchers;

In a project I am working on we are planning on using Zotero 2.0 to collaborate on compiling a database of archival sources. The ease with which individual collections can be shared in Zotero 2.0 makes it a very attractive alternative to the old system of swapping ZIP files of endnote libraries or worse still, emailing documents or reference lists back and forth for manual entry into your bibliographic software.

If you haven’t tried Zotero, then I suggest that you read this and decide whether you want to try the Beta or the current stable version. It takes no time to install and is completely free. Personally, I have found it to be an incredibly useful addition to my software suite and it is likely to soon completely replace the commerical bibliographic software I am currently using. I don’t think Zotero will change the way all archaeologists collaborate, however for key groups of web-savvy researchers I suspect Zotero 2.0 will be picked up very quickly because it provides what seems to me to be a rather unique set of tools not yet available elsewhere.

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Publishing with Google Earth and Google Map products

Note: this is a post that originally appeared at my old blog and generated a reasonable amount of interest there, so I am posting it again here.

Google Earth and Google Maps are both wonderfully useful resources for archaeologists and people in allied disciplines. Google Earth in particular is a quite a powerful little program largely because of its simple, intuitive interface and the fact that it is free. But can students, researchers or academics use these images from a copyright perspective?

(more…)

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FGIS: a useful (and free!) random and systematic sampling tool

Leszek at Free Geography Tools has written a brief post about using a freeware GIS tool (FGIS) that would be of some value for archaeos engaged in field sampling (on any scale). The tool allows you to create files containing either a series of random points or systematically spaced gridded points. Creating such files is a useful skill most archaeologists will need at some point: for example, I have used random and systematic points for field surveys (eg. to define centre points of areas to survey) or as part of a detailed recording or excavation sampling strategy (eg. to define 1 metre squares on large sites for detailed recording work).

The tool allows you to define a geographic area (polygon) that you would like to sample and then allows you to populate this with points. You can create a random or systematic (grid) distribution of points and can define both point spacing (for grids) or number of points (for random points). Resulting points can be saved as a shapefile, a common and mostly open GIS format as well as a few other formats.

Once you have your shapefile of points you can upload it to most GPS devices using DNRGarmin and similar Windows software, or GPSBabel for fellow Mac users. You can even covert it to display in Google Earth and print the resulting image with Lat/Long or UTM coordinates attributed to each point.

There are more advanced options for doing this with many commercial GIS applications but they’re not free and therefore less accessible for students. This method also seems rather low-tech, and low-tech is king on fieldwork in my experience! Also, if you are not already a regular reader of Leszek’s blog I highly recommend it as he writes about many useful tools for archaeos.

Links
Check out Leszek’s post here.

DNR Garmin website

GPSBabel

FGIS

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Research tools and the web: finding and keeping track of references

The internet has revolutionized the research process providing a range of new, on demand sources for scholarly articles. In today’s post I wanted to briefly look at some free tools for finding and keeping track of research sources on the web that I have found useful in writing a PhD and also working as an archaeological consultant.

Finding references: Google Scholar
Most people are familiar with Google Scholar, the search engine that retrieves information about research papers, books and so on. It can be incredibly useful, particularly if you are delving into a new field or research area and you quickly need to identify key sources. Scholar is reliant upon search engines having discovered a source in order for it to show up in your search results. Thus, if a source is not available on the web in the correct format then, logically, it does not show up in scholar search results and so searches on any particular topic might only return a small number of relevant sources available. Typically, there was a bias towards recent journal articles that were on the web.

This was once a real limitation to scholar’s usefulness. However, during the past two or three years things have changed as more and more academic sources – both new and old – are being posted to the web. Today, scholar is a powerful tool that returns relatively comprehensive results in many subject areas. You can search for articles by author as well as those which are published within specific journals or in a particular date range; results can be directly imported into your bibliography software (see below). It has its limits though and the number one limitation in my view is scholar’s inability to monitor your searches. At present it is not possible (easily and reliably at least) to monitor a particular search for new articles as they appear. For example, if I search for ‘coastal archaeology’ in December it would be useful for scholar to notify me when a new article appears in those search results in February.

If you’ve not used scholar for a while it is well worth revisiting. It is constantly improving and is (in my experience) the easiest way to quickly find relevant scholarly articles on the web today.

Zotero
(Zoh-TAIR-oh) is, in the words from their website, “a free, easy to use firefox extension to help you collect, manage, and cite your research sources”. It is an open source project based out of George Mason University and is free to install and use without restrictions. It serves three main purposes:

– Collecting sources. Zotero uses bits of code called translators that allow you to import citation information from a website automatically. Many popular journal databases and major libraries have working translators and more are being actively developed. The result: you can visit many major sources of references, search and find what you are looking for and with one click import these into your Zotero bibliographic database. In other words, no more manual entry of citation information into your bibliographic software!

Major journal publishers such as Elsevier as well as Google Scholar, Amazon and many, many other websites are supported.

– Manage your sources. Zotero imports your references into a database file on your Mac or PC which is accessed by using your firefox web browser. You can create folder hierarchies (Zotero calls them ‘collections’) in which you can store your references. Once you have a source in Zotero you can add tags (keywords), enter notes, create links to any website (e.g. to reviews of a book) and attach a link to a local file or web document. Figure 1 below shows the browser interface.

– Cite sources and create bibliographies. This part of Zotero is important as it allows you to directly cite a source from your database in a document, and automatically create a bibliography of sources cited. I use Word 2008 on a Mac, which is not supported yet, however this function works on most other versions of word and on all versions of open office. You simply install a small add-on, select the reference you want to cite, and you’re away.

With these sorts of options Zotero is emerging as a serious stable alternative to commercial bibliographic software such as Procite and Endnote. It’s clean, fast, stable and customizable. It’s web interface is its real strength. I use it mostly for importing references I find in google scholar: simply run a search on scholar, click the ‘Save to Zotero’ button and select the references to import.


Figure 1 – The Zotero interface

Citeulike
Citeulike is best compared to a social bookmarking utility for scholarly articles. Users create their own account and add articles to their library by using a small bookmarklet (a bookmark that opens a pop-up window – see Figure 2, below). This process is automatic for most major journal websites, and so once you find an article you simply click your bookmarklet and it is directly added to your library. Citeulike doesn’t yet have the functionality of Zotero so for example, you can not automatically add references from Google Scholar to your library, however most major journal databases do work well.

Citeulike has other advantages that make it a crucial part of my work flow at the moment, mainly because it supports web feeds. All users have a web feed, meaning that others can subscribe to your feed and be notified when you add a new reference. You can also create and subscribe to feeds published by groups, for example I have created the group “Archaeology and Palaeoenvironments of the Australia-Pacific” which is open for anyone to join. Any members of this group will be automatically notified of new references added to the group’s library. So, for me the great value of citeulike is that it makes it much easier to share references between people interested in similar areas.

Figure 2 – Citeulike bookmarklet pop-up

So in summary, my web workflow consists of the following:

1) find references in scholar, citeulike or by browsing journal websites;
2) add my reference to citeulike OR zotero depending on which platform allows me to automatically import my reference;
3) download the article PDF to my computer;
4) export the citation from Zotero or citeulike into my local endnote library (one click);
5) attach the PDF to the endnote item; and finally,
6) read!

It may seem like a lengthy process but in most cases it takes me only 1-2 minutes to find, import and cite a new reference using these tools. Zotero is rapidly improving and will soon allow users to share libraries, thereby replacing much of the functionality of citeulike. Although for many using these sorts of tools may be quite new, they are typically very easy to use and can speed up the time it takes to find and manage your research sources.

I’d be interested to hear from others who use these or other tools or have suggestions for improving this system. You can do so in the comments below.

Links:

Google Scholar

Zotero

Citeulike

My citeulike library

Citeulike group: archaeology and palaeoenvironments of Australia and the Pacific

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Download web maps to your garmin GPS

Readers may be interested in a new service from Garmin that allows you to download results from web-based mapping applications directly into your Garmin GPS device. Window’s Live and Google Maps both support the service which I suspect exports the results of web based searches for directions (i.e. drive 200 m to X road, turn left at Y street…) as a route then uploads this to the GPS.

It’s a simple browser plugin that works on Windows and the Mac and is apparently compatible with any Garmin GPS that is able to connect to your computer via USB. It’s free and can be found here:

http://www8.garmin.com/products/communicator/faq.jsp

I found this service on the  Free Geography Tools blog: if you have a background in archaeology, earth sciences or other allied fields and you use ‘maps’ (which will be all of you!) I highly recommend visiting. Many tips for free software, web services and so on.

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Arcview on a mac?

A little while ago I purchased a new macbook pro after discovering that they now run Windows. As far as laptops go, MBPs are brilliant: they take no time at all to to configure out of the box, are simple to use, backup and recover. They are wonderful as a writing and research tool and lets face it, the MBP looks cool as well.

Archaeologists however can never really move away from using Windows in some way. Various important software packages are only available on this OS: Sofware for radiocarbon calibration, survey, CAD, GPS and GIS are typically shackled to Windows. One of the most crucial Windows programs I use for research and consultancy work is Arcview. For the uninitiated, Arcview is a fairly capable and widely used GIS program that allows one to display, manage and analyse spatial data such as site locations, environmental data, infrastructure and development information and so on.

Arcview will only ever be a windows application and so jumping over to a Mac has mean that I needed to get Windows working on my Mac well enough so that I can seemlessly move between my Windows and Mac environments, without restarting my computer. Although this is all possible it has taken me a while to get it working well on my Mac and so in this post I simply wanted to highlight some key tips for people in similar situations.

  1. Bite the bullet and install bootcamp. There are other ways to run windows in a mac, without needing to partition your hard disk, but after multiple attempts I found that they were all really quite slow when it came to working with large datasets. Bootcamp will run any windows program at normal (i.e. ‘native’) windows speeds. Use it, it’s a free part of OSX.
  2. Give yourself space to move. When you create your bootcamp partition, give yourself at least 6 gigabytes for Windows PLUS whatever is required for your windows applications. If you think you will have 30 gig of data, give youself that much space. I initially tried leaving my arcview data on the Mac partition however it was very slow to load on the windows side and some datasets would not load at all. I then tried an external firewire hard drive which was faster, but still sluggish and caused other problems. With arcview at least, there is nothing as fast or functional as having your program and data on the same drive. Use an external drive for backups.
  3. Format your bootcamp partition in NTFS. Bootcamp guides will tell you that you must use FAT32: ignore that advice. There are benefits and disadvantages to both and despite what you read the main point is that both drives will be accessible from inside each operating system when you eventually install the VM software. Most importantly, if you use NTFS then you can very easily backup the whole bootcamp/windows installation using your mac and reinstall without a fuss when things go wrong. So, once you proceed to installing windows on your bootcamp partition make sure you tell the Windows installer to format your partition as NTFS.
  4. Purchase and install parallels. Once you have everything installed in bootcamp and Windows has done its crazy ‘update for 2 days’ thing, shut down Windows and restart your mac in OSX and then purchase and install parallels. After you install it on your mac running windows is very simple. You simply run parallels and then select ‘my bootcamp’ from the main menu and your Windows bootcamp install will open in its own window (which is resizable, etc). From here you can run arcview.
  5. Create a clean install recovery image. It may take a few days to get your Windows XP install and other software and external device drivers (GPS for instance) running. Once you are happy that you have the perfect set up then download a nifty little Mac program called winclone. This program makes a compressed copy (disk image) of your entire windows partition that includes all of your Windows updates, drivers and software. This backup image can be reloaded onto your NTFS Windows partition at any time so that you can quickly revert to a clean install without having to go through the entire process again. This is useful to two reasons. (a) Windows will eventually die on you at a very inconvenient time, thus requiring a full reinstall, and (b) if you find you need more or less space on your windows partition, you can resize the partition and reinstall a fresh copy of windows very quickly. I needed to resize my Windows partition from 10 gig to 40 gig and using Winclone, managed to do so in less than an hour!

And that’s it! After running arcview for several weeks this way I have not noticed any reduction in performance or any other errors, even with large raster datasets that often cause problems.

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Blogging for graduate students

John Hawks has an excellent series of essays on blogging, research and academia. John’s blog has been around for years – from at least 03 or 04 as far as I remember, and he’s also an active palaeoanthropologist. I must admit that not being a palaeoanthro, I find that some of his content is a little outside my areas of interest but I nevertheless do enjoy reading his blog. Anyway, the first couple of essays in his 4 part series are:

Graduate students and blogging

How to blog and get tenure

The most salient points for me is that blogging is not necessarily a bad thing for a professional to engage in and that there are some distinct benefits for graduate students who start out writing early in their careers. He writes:

I’d like to advocate for a model of blogging that many graduate students might find useful. If I were starting out today, I’d blog my dissertation. Why not? Is there really anything so secret in your history and literature review that it couldn’t be read by the few hundred people who will find your blog?

I think the other important point is that blogging is not research and one should not allow it to impact on writing grant applications, theses, publications and so on. He warns:

You start out writing a few posts about your work, and comment negatively on creationism. And then you spend your time online reading stupid posts from intelligent design blogs, just so that you can refute them. Soon your mind starts to decay, and then you can’t do your actual research anymore.

I run a small archaeology consultancy which is basically a full time job. I schedule dedicated time for my research and treat that time with the reverence it deserves, after all, at the end of the day what counts is the quality of the research I do and the level of my outputs – not my blog’s page rank or subscriber count. I approach blogging a little like the conversations that happen over coffee between sessions at conferences: a chance to talk informally about your research, recent news and new methods or ideas, as well as providing opportunities to meet new people. The great thing about the web though is that it is accessible to a much larger number of people with similar interests. There is a real potential for a blog to have negative impact on your career though. For example, gossip, poorly thought through arguments or just plain bad writing are just as damaging in a blog as they would be if you took the same approach to conversations at the conference bar.

Although I’ve been reading and commenting on blogs for years, this is the first time I have stuck with one (there were several abandoned attempts in 04 and 06), so I can’t really speak to the benefits of blogging yet. But John’s blog has been around for a good while and his tips and tricks are well worth taking note of. And if you’re an Australian archaeologist, consider starting something: as far as I am aware there are only a couple of active bloggers out there and the more the merrier!

Picture credits – Laughing Squid’s photostream on flickr (creative commons license)
Links – John Hawks Anthropology Weblog

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Archaeological survey and geotagging

As a consultant archaeologist time is always valuable and so it is important to have a robust system for recording and capturing field data quickly. By the same token, shoddy field recording practices result in mistakes and at best this results in lost time or a poor report, and at worst can lead to missed sites or poor management outcomes. So developing techniques to help achieve a good balance between efficiency and quality are critical and emerging digital technologies have a lot of potential in this area.

On large projects, there can be a lot of field data to record: site data (including multiple site types), varying survey methods, ground visibility, previous ground disturbance, environmental characteristics and so on. In addition to the paperwork keeping track of  digital photos and GPS data is also critical, after all an incorrect coordinate or photograph number can cause major problems when it comes time to write up your results long after you have left the field. Trying to fill out a range of different proformas and document your digital data can be difficult enough on its own, but the addition of other factors such as hot sun, high humidity and friendly insects really can upset the best field recording system.

Because of all this, I place a lot of effort into my recording system and in particular, over recent months I’ve been looking for ways to help manage my digital data. Particularly digital photos, GPS waypoints and GPS tracks recorded during a survey. One useful trick I’ve discovered is that it is possible to ‘sync’ or cross reference your digital photos and GPS data. Digital cameras automatically embed exif data within the digital image file, and this includes information such as camera settings, date, time and so on. Similarly, the ‘autotracking’ option on most handheld GPS devices records useful data with each point they record – whether that be an automatically created track point, user-created waypoint and so on.

For a while now I have used the exif and GPS metadata to help make sense of problematic digital photographs of sites or places where your paper record is in error (ie, an incorrect coordinate or site number). In this case, it is fairly straightforward process to cross-check the time and date of your waypoint or track point with the time and date of your photos, so that you can fill in the gaps in any missing information. It is a nice fall back position when your memory and field notes have partially failed you and although simple, it is generally quite a reliable way of verifying problematic data. Importantly though, you do need to make sure you have the time and date correctly set on your devices!

In recent years ‘geotagging’ software has started to emerge and these enable you to automatically embed coordinates recorded in your GPS into digital photos taken at around that time. In short, you tell the software where your photos and GPS data files are and the software will automatically sync the exif data from your digital images with the metadata on your GPS, thus generating a series of spatially referenced photos. There are a range of benefits to doing this: you can just use geotagging for maintaining and archiving your own photos, however for me the attraction is the potential for using geotagged photos to report on and communicate results with clients or other stakeholders (such as Indigenous Traditional Owners or the broader community). In a consulting context, this method has potential for presenting your results in a more interactive and interesting way. For example, it is possible to send your geotagged photos to free web or software applications (via Google Earth or Google Maps) so that they display in an interactive format.  With the addition of survey results (eg. site data, survey locations, development areas, etc) it should be possible to create an interactive presentation for your client or others that could be uploaded to the web, sent on a disk or so on.

Geotagging has a lot of potential to help archaeologists with managing their field data and I’ll write more about my trials in this area in future. For web veterans who’ve been following trends in web technology over the past few years, this is all probably be nothing new however I’m yet to see archaeologists talk openly about how their experiences using these types of things. What other ways are archaeologists  using these and other technologies to help with recording and managing field data? Let me know in the comments below!

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