GIS For Biologists

This is the companion webpage for GIS For Biologists: A Practical Introduction For Undergraduates by Colin D. MacLeod (you can find out how to purchase this book by clicking here). This page is hosted by GIS In Ecology, one of the world leaders in providing GIS training to biologists, and on it, you not only find the the link from which you can download the data which are used for each practical exercise in the book, you will also find information about downloading and installing the required GIS software, and links to free short videos which accompany each chapter and practical exercise. These videos will help you understand more about how to use GIS in biological research, and provide additional help for completing each practical exercise. There are also links to other useful information on the GIS In Ecology site, such as case studies on how GIS is used in biological research, where to find data for use in GIS projects and FAQs, and information on developing your GIS skills.

1. Downloading And Installing Your GIS Software:

When working through the practical exercises in GIS For Biologists, the first thing you need to do is download and install either ESRI’s ArcGIS For Desktop GIS software package (which you may need to purchase a licence for) or QGIS (which is free).

The choice of software is up to you, and will not affect what you learn from GIS For Biologists, but if you want some help with deciding which is best suited for your specific needs, then this video may help. In addition, if you are working on a computer which is running either a Mac OS or Linux, then you may be better off using QGIS as there are versions of QGIS specifically for these operating systems.

ArcGIS For Desktop is a commercial GIS software package, but you can get a fully functional 60 day free trial version from here. ArcGIS can only be installed on computers running a Windows operating system (either as the main operating system or as a virtual machine). The instructions for the practical exercises in GIS for Biologists were written specifically for ArcGIS 10.3 (the current version when the book was published), but they will also work with ArcGIS 10.1 and 10.2, and should work with ArcGIS 10.4 (the latest version – although this has not yet been tested). They will not work with earlier versions of ArcGIS For Desktop, or with ArcPro or ArcGIS Online. In addition, some of the exercises will require tools from the Spatial Analyst extension, which may require a separate licence. To install ArcGIS 10.3 For Desktop, follow the instructions hereNOTE: In almost all cases, you will be setting it up as a Single-Use Licence, so make sure you follow the instructions for this option and not the ones for Concurrent Use Licence users.

QGIS, also known as Quantum GIS, is a free, open source GIS package. There are versions of QGIS for Windows, Mac Os, Linux and Android operating systems (although the Android version cannot currently be used for the exercises in GIS For Biologists). While you can download through from the QGIS project homepage, you will have fewer problems if you use the links provided below as these will take you directly to the appropriate version for using with the instructions for the exercises provided in GIS For BiologistsNOTE: If you choose to download QGIS via QGIS project homepage, please make sure that you download and install QGIS version 2.8.3 (for Windows users) or 2.8.4 for (Mac OS users) and not any other version – even if newer ones are available – as the instructions may not work for other versions. If you try QGIS and find it useful, please consider donating to the QGIS project to help support its future development. Even ff you do not have the funds to make a donation, you can still support QGIS by getting involved in other ways.

If you are using a Windows computer, click here to download the 64 bit version of QGIS 2.8.3, or here to download the 32 bit version of QGIS 2.8.3. If in doubt as to which version to install, try the 64 bit version first, and only if this does not work on your computer, try the 32 bit version. To install it, follow the instructions here. Alternatively, watch a video which show you how to download, install and set up QGIS here.

To install QGIS on a computer running a Mac OS, download a compressed file containing the QGIS .dmg file for version 2.8.4 clicking here. Once you have downloaded it, open the folder and install the .dmg file called QGIS-2.8.4-1.dmg. NOTE: You will probably need to change the security settings on your computer to allow you to install software from an unauthorised source before you can install QGIS. If you run into any problems, this video may help (this is not a GIS In Ecology video). The other .dmg files provided in this compressed folder are optional, but it is worth installing them too, after you have installed QGIS. If you choose to install these files, install them in the following order: NumPy-1.8.0-1.dmg, NumPy-1.9.2-1.dmg, SciPy-0.13.1-1.dmg, SciPy-0.16.0-1.dmg.

Once you have installed your chosen GIS software package, make sure you read chapter eleven of GIS For Biologists so that you understand the layout of its user interface. You can also watch the videos which accompany this chapter here (for ArcGIS 10.3 users – this is not a GIS In Ecology video) or here ( for QGIS 2.8.3 users), but you still need to read chapter eleven to ensure that you set the user interface for your GIS software in a way that is compatible with the instructions for the practical exercises in GIS For Biologists.

NOTE: If, when using QGIS on a Windows computer, you find that you have trouble accessing the GRASS tools (e.g. the V.TO.RAST.ATTRIBUTE tool for step 3 of Exercise Three – which starts on page 186 of GIS For Biologists), the most likely reason is that you have installed the 32 bit version of QGIS when you should have installed the 64 bit version. To solve this issue, uninstall your current version of QGIS and then download and install the 64 bit version of QGIS 2.8.3 from here.

2. Data For Practical Exercises InGIS For Biologists:

Before you can do any of the practical exercises in chapters twelve to seventeen of GIS For Biologists, you need to download the compressed folder which contains all the data which are to be used in them. To do this, first create a new folder on the C: drive of your computer (assuming you are using a computer running a Windows operating system – if you are using a different operating system, you will need to create this folder elsewhere and change the folder addresses provided in GIS For Biologists accordingly), and rename it GIS_FOR_BIOLOGISTS. Next, click here and save the compressed file to the folder you have just created (which should have the address C:\GIS_FOR_BIOLOGISTS). Once this file has been downloaded, open the compresses folder, copy its entire contents and paste it into the folder C:\GIS_FOR_BIOLOGISTS. Once you have done this, you are ready to start working through the practical exercises in GIS For Biologists. A video showing you how to download and unzip this compressed folder on a computer running a Windows operating system can be viewed hereNOTEYou only need to download and unzip this compressed file once as it contains all the files you need to complete every exercise contained in section two of GIS For Biologists.

3. GIS For Biologists: A Practical IntroductionOnline Course: GIS In Ecology is currently developing an online on-demand video course based on the practical exercises in GIS For Biologists: A Practical Introduction For Undergraduates. When this is launched, a link to it will be posted here.

4. Free Short Videos To Accompany Individual Chapter And Practical Exercise:

Unless otherwise stated, the videos for the following links are hosted on the GIS In Ecology You Tube Channel. When additional videos are posted, new links will be added to the appropriate sections below. Additional helpful tips videos can also be found on the GIS In Ecology You Tube ChannelNoteWhile these videos are primarily aimed at QGIS users, ArcGIS users may also find them useful.

Free Videos For Chapter One: Examples of biological research projects that have used GIS: Species distribution modelling and GIS: a case study on Cuvier’s beaked whale in the Bay of BiscayAn introduction to using Google Earth as a data viewer for conservation practitioners.

Free Video For Chapter Two: A video for this chapter will be added shortly.

Free Videos For Chapter Three: What are projections and why are they important in GIS?Accuracy, precision and resolution for GIS data.

Free Videos For Chapter Four: What are projections and why are they important in GIS?Setting A projection/coordinate system for your GIS project in QGISHow to transform a data layer into a different projection/coordinate system in QGIS.

Free Video For Chapter Five: A video for this chapter will be added shortly.

Free Videos For Chapter Six: Setting A projection/coordinate system for your GIS project in QGISHow to add a existing data layer to a GIS project in QGISHow to transform a data layer into a different projection/coordinate system in QGISThe ‘shapefile approach’ vs the ‘geodatabase approach’ to GIS.

Free Video For Chapter Seven: A video for this chapter will be added shortly.

Free Video For Chapter Eight: A video for this chapter will be added shortly.

Free Videos For Chapter Nine: How to set up a GPS receiver to collect biological dataHow to transfer data between a GPS and a GIS projectHow to install an app to turn a smart phone into a GPS receiverHow to record a waypoint on a smart phone using the GPS Essentials appHow to record a track on a smart phone using the GPS Essentials appHow to set your smart phone to record high resolution spatial data.

Free Videos For Chapter Ten: ArcGIS or QGIS: Which is better for biologists?An introduction to the ArcMap user interface (this is not a GIS In Ecology video); Downloading and installing QGISDownloading, installing and setting up QGIS (this is not a GIS In Ecology video); An Introduction to the QGIS user interface.

Free Videos For Chapter Eleven: An introduction to the QGIS user interfaceAn introduction to the ArcMap user interface (this is not a GIS In Ecology video)

Free Videos For Chapter Twelve: How to add a existing data layer to GIS project in QGISHow to change the way a data layer is displayed in a GIS project in QGISAn introduction to using Google Earth as a data viewer for conservation practitioners.

Free Videos For Chapter Thirteen: How to install plugins to extend the functionality of QGISHow to make a new data layer in a GIS project using QGISHow to transfer data between a GPS and a GIS projectHow to make a new GIS data layer using the Google Earth user interface;How to transfer data layers between Google Earth and a GIS project.

Free Video For Chapter Fourteen: How to install plugins to extend the functionality of QGIS.

Free Video For Chapter Fifteen: Setting A projection/coordinate system for your GIS project in QGISHow to transform a data layer into a different projection/coordinate system in QGIS.

Free Video For Chapter Sixteen: How to make you own custom polygon fill styles for use in GIS projectsHow to make your own custom symbols for use in GIS projectsHow to create and use custom style files in QGIS.

Free Video For Chapter Seventeen: An introduction to using Google Earth as a data viewer for conservation practitioners.

5. Links To Other Useful Pages On TheGIS In Ecology website:

Below are a series of links to other pages on the GIS In Ecology website which you might find particularly useful. These pages, and others can also be accessed through the buttons on the menu bar on the left hand side of this page. You can return to this page at any point by clicking on the GIS For Biologists button on this menu bar.

I. Case Studies on Using GIS in biological research: This page provides links to a series of case studies on the use of GIS in biological research. These come both from projects which Colin D. MacLeod (the author of GIS For Biologists) has worked on, and the research projects of other people. They demonstrate the range of biological research questions which can be examined using GIS.

II. Source of data for biological GIS projects: This page provides links to a variety of free sources of data which can be included in GIS projects, including information on elevation, water depth, remote sensing data, country outlines and so forth.

III. Useful links for biological GIS users: This page provides links to a variety of resources which biological GIS users may find useful.

IV. Useful Tools for biological GIS users: This page provides links to a number of Excel workbooks created by Colin D. MacLeod, and others, which are designed to help do specific tasks, such as converting latitude and longitude data into decimal degrees and estimating the positions of animals, plants or objects using information on bearing and distance.

V. Frequently Asked Questions (FAQs): This page provides answers to a variety of frequently asked questions about the biological use of GIS, and aboutGIS In Ecology.

6. Developing Your GIS Skills:

GIS For Biologists is designed as a primer to show undergraduates, and other novice biological GIS users, how useful GIS can be in biological research, and to provide a starting point for learning basic GIS skills. However, GIS is an incredibly powerful tool for biologists and it can be used to investigate a wide variety of research topics. Therefore, once you have learned some basic GIS skills from GIS For Biologists, you will no doubt want to expand your GIS knowledge.

There are a number of ways you can do this. One of the most powerful is to simply take a leap into the unknown and start playing around with the various tools available in your chosen GIS software, or to search the internet for information on how to do various tasks you are interested in doing. There are many places where you will find instructions on how to a large variety of tasks, including a large number of forums, where you can ask question if you get stuck. Of these forums, some of the most useful are the GIS StackExchange and the GIS In Ecology Forum.

If you prefer to develop your GIS skills in a more directed manner, there are a variety of other GIS books in the PSLS series which will help you work out how to do a variety of specific tasks and how to investigate a range of biological research questions. These books use the same task oriented learning approach based on flow diagrams which you will already be familiar with from GIS For Biologists. At the moment, these are primarily aimed at marine biologists, but the same basic skills can be transferred to many other areas of ecology and biology. In addition, while these books primaarily use ArcGIS GIS software as their example software, they are structured in such a way that it is relatively easy to transfer them to other software packages, including QGIS.

You can find the full list of these books, and information on where to buy them, here, but they include workbooks on how to investigate the home ranges of individual animalshow to integrate GIS and species distribution modelling (SDM) and how to create high quality maps for reports and presentations and how to start creating your own custom GIS tools for biological research. There is also a larger volume which contains instructions on how to do over 100 tasks that biological GIS users are likely to need to be able to do on a regular basis. However, while this larger volume contains instruction sets based around flow diagrams for these tasks, the introductory chapters are slightly extended versions of those in GIS For Biologists, and you should be aware of this repeated content.

Finally, there are a variety of places where you can take courses to develop your GIS skills. These include dedicated graduate courses and masters degrees, and courses by software manufacturers, such as ESRI (the makers of the ArcGIS software package). However, such courses need to be selected with care as often they will be targeted at terrestrial geographers or business users rather than biologists, and you need to ensure that you will learn useful skills which can be applied to biological research before signing up for them.

GIS In Ecology also runs a variety of courses dedicated to teaching GIS skills in a biological context. Again, these courses use the same task oriented learning approach based on flow diagrams as used in GIS For Biologists. At the current time, these are primarily run in Glasgow in Scotland and are not available elsewhere, but this may change in the future. In addition, we are also in the process of developing online, on-demand courses, and information on these can be found here once they are available.