GIS For Biologists

Total video running time: 63 minutes; Estimated practical working time: 3 hours.

This exercise consists of thirteen videos which will introduce you to raster data layers (also known as gridded data layers), how biologists typically use raster data layers in their research, and how you can create them in a variety of different ways in a GIS project. It is designed to accompany chapter fourteen in GIS For Biologists: A Practical Introduction For Undergraduates, and you will require a copy of this book in order to be able to complete this exercise successfully. This book is available as a paperback and a Kindle eBook, and you can find out where to purchase it by clicking here. This exercise, and the accompanying videos, do not need to be completed in a single session, and if you are feeling tired, are developing eye strain, or are just in need of another cup of coffee, feel free to take a break between videos whenever you please.

If you have not already subscribed to on-demand videos for this exercise, simply click play on the first video below and you will be provided with the option of purchasing a subscription. The payment system is operated by Paypal, but you do not need a Paypal account to use this payment option. These payments are processed by GIS In Ecology, which operates GIS For Biologists. Note: Your subscription will only last for three months from the date that you subscribe. Therefore, you should not subscribe until after you have received your copy of GIS For Biologists: A Practical Introduction For Undergraduates. If you wish to try a video before you purchase a subscription, the free video for this exercise is Video Six, and it covers how to set the projection/coordinate system for your data frame at the start of this exercise.

Before you start working through this exercise, please ensure that you have the required version of QGIS installed on your computer (for Windows users, this is version 2.8.3, while for Mac OS users, this is 2.8.4). You can find out how to download the required version of QGIS from here. You will also need to ensure that it has been set up to use the standard format which will be used in the videos below and that you are familiar with the terms that will be used to refer to the various sections of the QGIS user interface (see our Getting Started page and chapter eleven of GIS For Biologists: A Practical Introduction For Undergraduates. In addition, please read through the introductory information for this exercise on pages 155 to 158 of GIS For Biologists: A Practical Introduction For Undergraduates. Once you have read through this information, you can move onto video one.

At the end of this exercise, you will find an optional extra which you can use to test the GIS skills you have learned in it. If you have subscribed to the videos for a whole a course (rather than an single exercise), you can also choose to submit the results of this optional extra for assessment so that you can received a certificate of completion for the course you subscribed to. More information how this assessment process works is provided in the optional extras section towards the bottom of this page.

Information about how to get help and support with this exercise can be found at the very bottom of this page.

Video One – Introduction to the exercise:

This video will provide a brief introduction to this exercise, including information about what a raster data layer is, how they compare to the feature data layers you used in exercise two, why raster data layers are useful, how you can make raster data layers from existing feature data layers and the five raster data layers you will create as part of this exercise. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Video Two – Downloading the data for the exercise:

If you have previously downloaded these data for use with a different exercise hosted on this site, then you do not need to repeat this step, and you can move directly on to Video Three. If you have not previously downloaded these data, then this video will show you how to download the data required for this exercise and add it to a folder on the C:\ drive of your computer called C:\GIS_For_Biologists (Note: This assumes that you are working on a computer running Windows. If you are using a computer running Mac OS, you can place this folder on your desktop or Macintosh HD folder.) This will be the folder which you will use to save all the data which you will use in this exercise, and throughout the rest of the exercises on this site. This information is also detailed on pages 157 and 158 of GIS For Biologists: A Practical Introduction For Undergraduates. These data can be downloaded from here. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Video Three – The data layers that you will use:

This video will introduce you to the feature data layers which will be used in this exercise. Information about these data layers can also be found on page 158 of GIS For Biologists: A Practical Introduction For Undergraduates. If you have followed the instructions in video two of this exercise correctly, the files for these data layers will be saved in the folder called C:\GIS_For_Biologists (or your folder of the same name, but stored in a different location, if you are a Mac user). Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Video Four – The starting point for the exercise:

This video will outline the starting point for this exercise and will ensure that you have everything ready to begin it. This information can also be found on page 180 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Video Five – The steps you will complete in this exercise:

This video will take you through the seven steps you will complete as part of this exercise. The detailed instructions for these steps start on page 180 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Video Six – Step One: Set the projection and coordinate system of your data frame:

The first thing you should do when you start any new GIS project is to set the data frame (i.e. the blank map on which your data will be plotted) to use an appropriate projection and coordinate system. Details of the one which will be used for this exercise can be found on page 180 of GIS For Biologists: A Practical Introduction For Undergraduates. The video below will show you how to set a GIS project in QGIS to use this specific projection/coordinate system. The flow diagram outlining this process can be found on pages 181 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise. Note: This video is free to access to allow you to try our training materials out before you purchase a subscription to this exercise.

Once you have completed this step, check the projection/coordinate system for your GIS project by following the process outlined on page 182 of GIS For Biologists: A Practical Introduction For Undergraduates. If your GIS project is not set correctly, you will need to go back and repeat this step. If it has been correctly set, you can move onto video seven of this section.

More information on projections, and how to select an appropriate one for your own GIS projects can be found on our Getting Started page and in chapter four of GIS For Biologists: A Practical Introduction For Undergraduates. In addition, information on how to find out more about the Proj.4 strings used to set projections and coordinate systems in QGIS can be found on pages 182 and 224 of GIS For Biologists: A Practical Introduction For Undergraduates.

Video Seven – Step Two: Add any existing data layers you need to create your raster data layers to your GIS project:

This video will take you through all the steps which you need to carry out to add an existing data layer to your GIS project. The flow diagram outlining this process can be found on pages 183 and 184 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the image on page 185 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video eight of this exercise.

Video Eight – Step Three: Create a raster data layer of land elevation:

Creating a continuous surface of land elevation is one of the most common processes that biologists need to do when working with raster data layers. This video will take you through all the steps which you need to carry out to create such land elevation raster data layers. The flow diagram outlining this process can be found on pages 186 and 187 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the image on page 188 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video nine of this exercise.

Video Nine – Step Four: Create a raster data layer of slope:

Once you have created a raster data layer of land elevation, you can then use it to derive a range of additional raster layers. In this step, you will derive a raster data layer of slope from the land elevation data layer created in step three. The flow diagram for this step can be found on pages 189 and 190 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the image on page 191 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video ten of this exercise.

Video Ten – Step Five: Create a raster data layer of hillshade:

Hillshade measures how much direct sunlight a specific location will receive based on the local land elevation and the position of the sun on a particular date and a particular time of day. The flow diagram for this step can be found on page 192 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the image on page 193 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video eleven of this exercise.

Video Eleven – Step Six: Create a raster data layer of distance to the edge of the rainforest:

As well as deriving additional raster data layers from land elevation data, raster data layers can also be derived from other types of data layers. In this step, you will create a raster data layer that will measure the distance between individual grid cells and the edge of the rainforest which covers the top of Mount Mabu. You will also learn how to mask a raster data layer so that it only contains information for a specific area. The flow diagram for this step can be found on pages 194 to 196 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the images on page 197 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video twelve of this exercise.

Video Twelve – Step Seven: Create a raster data layer representing the extent of the rainforest area on Mount Mabu in 2013:

Up to this point, you have been working with environmental raster data layers which have been interpolated from feature data layers to create additional information. However, you can also simply convert a feature data layer into a raster data layer. In this step, you will use this ‘convert to grid’ approach to create a raster data layer which represents the area covered by rainforest on Mount Mabu in 2013. Such data layers can be used as a monitoring tool to assess the impact of human activities, such as logging or clearing rainforest for agriculture, on remote locations at relatively low cost. The flow diagram for this step can be found on pages 199 and 200 of GIS For Biologists: A Practical Introduction For Undergraduates. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to continue with this exercise.

Once you have completed this step, check the contents of your MAP window against the images on page 201 of GIS For Biologists: A Practical Introduction For Undergraduates to ensure that you have completed it correctly. If this is not how the contents of your MAP window looks, you will need to go back and repeat this step. If the contents of your MAP window look correct, you can move onto video thirteen of this exercise.

Video Thirteen – A review of the GIS skills you have learned in this exercise:

This video will review the five key GIS skills for using GIS in biological research that you have learned in this exercise. Note: If you cannot view the video in the window directly below this text, or if you cannot hear the sound when it plays, click here for an alternative method of accessing it. However, you will have to return to this page once you have finished watching it to complete this exercise.

Once you have viewed video thirteen, you have completed this exercise.

Optional Extra

Our optional extra sections offer you the chance to test out your newly aquired GIS skills by completing an additional task based on the GIS project you have been working on. To do this, you will need to refer back to the instructions for the main exercise and work out which parts you will need to adapt to complete it. In some cases, you may also have to refer to the instructions for a step in another exercise to find the specific block of instructions you are looking for. However, by doing this, you will learn how to take the knowledge you have gained by completing an exercise and use it to answer new biological questions using GIS. If you have subscribed to our short course, rather than just this exercise, you will be eligible to submit the completed optional extra for this exercise (along with those from the other two exercises) for assessment to gain a certificate of completion for this course (see below for more information).

For exercise three, the optional extra involves creating a raster data layer of the distance of each cell within the rainforest area from the summit of Mount Mabu (as indicated by the location of the single point in the point data layer called MOUNT_MABU_SUMMIT). This can be done by adapting the instructions for step 6 (see page 194 of GIS For Biologists: A Practical Introduction For Undergraduates), so that you will use the MOUNT_MABU_SUMMIT data layer as the starting point rather than the MOUNT_MABU_RAINFOREST_EGDE data layer you used originally. You will also need to make sure that you use new, and appropriate, names for your data layers to that you do not overwrite any existing data layers that you wish to keep. In addition, you will also need to ensure that you mask your initial distance data layer to remove those cells which fall outside of the actual rainforest area, leaving you with distance values for only those cells which fall within the rainforest itself. Once you have made this data layer, you will need to create a map from your GIS project using the PRINT COMPOSER window which shows this new distance data layer in the context of the surrounding landscape features. You will have to decide exactly which settings you will use for this map, and you can create it by adapting the instructions in step 4 of exercise one (see page 99 of GIS For Biologists: A Practical Introduction For Undergraduates).

If you wish to submit your optional extras for assessment so that we can send you a certificate of completion for this course, this will cost an additional US$15 (to cover administration costs as the outputs from each optional extra have to be manually inspected by a real person to assess whether they are correct or not), plus shipping costs for your certificate, which will vary depending on where in the world you are based. The optional extras for all three exercises must be submitted at the same time. To do this, export your final map for each exercise as a .jpg and save it into a compressed folder with the following name: [yourname]_GIS_Course_1_Optional_Extras. You can then send us this compressed folder as an attachment to colin(at)GISforBiologists.com, using the subject line GIS Course 1 Assessment Submission.

Once we receive your submission, we will check that you are eligible for assessment (i.e. whether you have a valid subscription to the videos for the whole course rather than an individual exercise), then email you to let you know whether you have passed and, if you have, exactly how much it will cost to issue and mail your certificate to you, along with a link which you can use to pay this fee. Once your payment has been received, we will issue your certificate of completion. This certificate will be individually numbered and embossed with the GIS In Ecology logo to prevent fraudulent reproduction. We will also maintain a database with information of participants who have been issued certificates of completion so that we can verify the validity of any certificate on request.

Help And Support

If you run into any problems with this exercise, the first step is to check the version of QGIS that you are using. It should be QGIS 2.8.3 (for Windows users) or 2.8.4 (for Mac OS users). If you are using any other version of QGIS, then you will need to install the correct one. You can find out where to download this version of QGIS from here. Once you have checked which version of QGIS you are using, then re-read the written instructions for the steps you completed before you encountered a problem and check that you have completed them properly. If this doesn’t solve your problem, then check the questions which have already been asked and answered below.

If, after checking all this, you still haven’t found a solution to your problem, then feel free to submit it as a comment in the comments section below (headed Leave a reply). When submitting a question, please make sure that you mention whether you are using a computer with a Windows or Mac OS operating system and which version of the operating system you have. As a spam-prevention measure, all comments on this page are moderated before they are posted. As a result, there may be a delay between when you post your comment, and when it appears. Once your comment has been successfully moderated, we will aim to respond to it within twenty-four hours. Note: Only comments that are directly related to problems with this exercise will be accepted and answered. If you have a more general question about the use of GIS in biological research, please visit the GIS In Ecology forum, where we will be happy to respond to such question