Tuesday, 3 June 2014

Data standards and intro to taxonomic databases


We will review the following this afternoon.

Taxonomic data standards please see the compulsory reading on the main blog
Install and explored Brahms herbarium database please check the main blog for the download links.

See you later

Tuesday, 20 May 2014

Relational database concepts and exercises

We will discuss the main concepts of relation database design in class

Please take a the main blog content on relational databases

Then you will be required to create a small relational database for invasive species. You will work in groups of three.

Please take a look at the invasive species database task - note this year this is not one of your course assignments so you will not be required to include all the details we will set up the tables for the database as an

Compulsory reading

Paul J. Morris (2005) Relational Database Design and Implementation for Biodiversity Informatics. You will find all the concepts in the introductory section of the paper. It then goes on to discuss the specialized taxonomic database concepts.
Bruce Maxim SQL Design and Implementation (ppt) this power point discusses SQL which we will take a look at in class and use in the exercise below.

There are also additional readings on the main blog page  

Assignment 3 - Using the BGIS for Landuse Decision Support Instruction


In this assignment we will use a spatial information portal and see how well constructed spatial models (maps) based on large amounts of  biodiversity data can be used to help guide decision making for land use and thus better and hopefully more wise use of the landscape on which we depend for survival.

I have provided four development so please work in groups of  three and one of two. Each group will choose one of the developments described below and analyse it for biodiversity "red flags" using SANBI's BGIS spatial information portal. This would be one of the initial steps you would take in an environmental assessment where biodiversity may be of concern. You can use the Planning and Assessment section of SANBI's Biodiversity Adviser website for background on environmental assessment and how BGIS may be used.

PLEASE NOTE: You may not use the Land Use Decision Support Tool for this assignment - I can check whether or not you did so beware!

What you must do:
1. Find the area or property mentioned in the development description
2. Find out which is the most appropriate Systematic Biodiversity Conservation Plan to use for this area and analyse it for the foot print of  your development. Hint all of South Africa is not represented on BGIS with a by Systematic Biodiversity Conservation Plans, don't panic if your area has less information than others.
3. Analyse at any other appropriate spatial information which may be of importance (both national or regional.
4. Download this excel spreadsheet and enter your decision, recommendations (if any) and justification and its supporting information from BGIS in the appropriate places
5. Using the BGIS online map tools create a pdf map for each point you make in your justification of your decision. Use the mark up tools to clearly indicate what you are saying.
6. Each group (i.e. only a single email per group) must send me an email with their excel spreadsheet and pdf maps attached by Tuesday 27 May.
Subject: BIM Honours Assignment 3 Biodiversity assessment
In the body include
a. Development chosen
[Development number][Development name]
b. Students in the group
[student name 1][student number 1]
[student name 2][student number 2]
[student name 3][student number 3]
7. At 9h00 on Tuesday 27 May each group will present their decision on the development with its justification illustrated using the pdf maps you created.

Note: we will check what the LUDS tool reports for each development only after the report back session. Doing this should help you to understand an important concept in biodiversity information management which we will discuss. Don't cheat I am watching you!

I had fun creating these irreverent example developments for you. Have fun with you presentation on Tuesday 28 and entertain us all, be creative but make sure that your reasoning is sound and based valid information from BGIS.

Development 1 
The Gupta Family Private International Airport-Cassino and Refreshment Centre

After the media scandal of recent weeks, the Gupta family has acquired several properties near the Lost City in North West. Amazed that they should have to comply with any environmental regulations when they own the land which is to be developed their lawyers have begrudgingly submitted the family’s plans to the provincial administration. Authorities for the North West were stunned to see that the plans are for a modest but well appointed international family airport where they can land their four family Airbuses and relax for 15 to 20 minutes before being transported by stretch Hummer limousine to the Place of the Lost City which they believe to be a boni fide archaeological wonder. The developments will include a 2000m long runway stretching in a North North Westerly direction from S25°19’6”, E27°12’0”. Parking for fifty limos and fifty five private security vehicle will be provided but parking for any police cars was deemed unnecessary. The airport building  will cover an area of 250000 square meters and will include a small hospital in case cousin Raj aged 12 and learner Airbus pilot overshoots the runway and a reluctantly added immigration check point. The comfort of the passengers on arrival and before embarking has been reduced to the bare necessities; a casino with twenty roulette tables, a hundred seat IMAX cinema and modest amusement park with a triple loop roller-coaster.

Development 2    
The Justin Beeber Monastic Game Lodge

On his recent trip to South Africa Justin Beeber visited to a small game lodge outside Johannesburg where he met a friendly zebra called stripy. Stripy ignited in him an epiphany, he has changed both his hair style (the tonsure is soon to hit the style channel big time) and his life style by becoming a Franciscan monk. He too is now a Beleeber. To accommodate his new way of life and promote his latest album, Do little rising, Justin’s legal team have snapped up a large property in Limpopo and several of the neighbouring properties may also be added if the development proceeds. These lie on the south side of the R36, eight kilometers from Tzaneen in the direction of Lydsdorp.
Here Justin plans a life of quiet seclusion at a monastic Game lodge along with stripy, his 30 newly acquired mares and fifty fellow teenage friars. Sources within the Holy See have confirmed that Justin will be the Monastery’s first abbot but have denied any rumors of the recent receipt of an exceptionally large tithing paid from the Bank of Canada. The contemplative buildings on the property will for now include a moderately sized basilica lavishly decorated with Carrera marble and onyx striped floors long the 300m long nave in honour of Stripy’s purity and steadfastness and stained glass windows in the sanctuary depicting scenes from the Saint’s life in Assisi.  Accommodation for the friars will be a spartan affair each cell featuring only a double bed provided with 400 count Egyptian cotton bedding and a  “braaikamer” with Bang and Olufsen entertainment centre, Weber, and a six man Jacuzzi. Bathing however will be at the communal gym and steam bath while sustenance will be provided at the refectory where Gordan Ramsey will monitor the quality of the frugal 4 course haute cuisine meals and read lessons from the Wisdom of Solomon. The new abbot’s mans, will be an entirely unpretentious abode lending its floor plan from Elizabeth II’s residence at Sandringham. In order not to disappoint fans the abbot will have at his disposal a 50000 seat auditorium with parking for 20000 motor cars. In total the development’s architects have assured environmentalist that it will blend into the local bushveld and will only occupy a mere 4 000 000 square meters.

Development 3
The Tyger Woods Young Ladies Golfing Academy with Personalized Tuition

Mindful of the fact that so few sporty, attractive, young South African women between the ages of 17 and 24 choose golf as a sport of choice Mr Woods ever generous with his exceptional talent has committed himself to provide these young women with a futures on the international golfing circuit. His legal team assures him that his personal coaching and mentoring of 50 of the most talented (and becoming) of these young golfers is bound to buff up his somewhat tarnished reputation in the world’s sport media. Mr Woods, also a keen gardener, has requested lawyers to investigated the feasibility of situating the academy in the Garden Route due to its superb climate and perfect soils. The property with the 21 digit code C039000000000293000000 has been ear marked as a possibility. In order that parents should have no concerns about their daughters' chastity, safety or sobriety while attending the academy it will allow only female teachers and support staff onto the premises apart from Mr Woods himself of course. The facilities where teaching and learning will be undertaken will include; an extensive naturally shaped swimming pool with spa area and grotto surround by exotic plantings, a beauty treatment centre run by Kimora Inc and a bikini emporium. Apart from the doubled beds with a plentiful supply of goose feather continental pillows the student dormitories will have a central a trampoline to encourage a fitness centred lifestyle. For the time being Mr Woods does not feel he should be concerned about his own accommodation on the estate and will generously "make do". Oh! there will be a 18 whole golf course with a clubhouse disco and ladies bar. The entire development should only occupy 25 000 000 square metres no more.

Development 4
Kardashian Environmental Education and Acquisition Destination

Due to a sudden, inexplicable and as yet unexplained intrusion of a combination of cognizance, consciousness and conscience the Kardashian family has taken its first steps towards sentience and become aware that the planet and therefore the future of the shopping mall may be in jeopardy. They have unanimously decided that they wish to contribute a portion of their newly acquired largess towards the prevention of  the wholesale destruction of its biodiversity. Besides which they never buy anything wholesale. A team of fifty environmental advisors has been assembled to investigate possibilities of where they can make a difference to the environment and while not encountering too many arachnid or reptilian horrors as even in Jimmy Choos running in high heels is not relaxing. The team has suggested the mega-biodiverse Western Cape in South Africa as a focus for the first project. The facility which will have a renosterveld theme.and house their usual anchor tenants i.e. Fendi, Versace, Gucci, Prada and a Kim and Kourtney Boutique but with greatly reduced floor space occupying only 80% of the total. This proudly makes this destination a green shopping mall because a full 20% will be groundbreaking environmental experiences including a Hemp Emporium and an organic food delicatessen near to the central 10 000 seat environmental venue and its 200m long catwalk. Here environmental experience seekers sometimes incorrectly called shoppers can keep up to date with trends in green fashion. The team feels property at -33.7057, 18..9027 will be ideal for this development due to its location on the Paarl Wine Route with its wealthy visitors and farmers. They are sure that the benefits to education will not be outweighed by the cost to the environment by this aesthetically pleasing 6000000 square meter intrusion into the landscape. Note  70% of  this footprint is earmarked as parking but will be offset by a pleasing biodiversity roof planted with magenta bougainvillea, Kim’s favourite. There should just be enough space on the roof for a solar panel to heat Khloe’s personal shower yet another green adddition to the building.

Biodiversity GIS (BGIS) and Environmental Impact Assessment (EIA)

You will be shown the BGIS web-portal in class, we will discuss what it is, how what its main purpose is, how to use it and the data and information it contains.

Please take a look at the main blog page

All the links on the main blog page are compulsory reading you should do before you start with
Assignment 3: Using the Biodiversity GIS Information portal for Landuse Decision Support
which comprises10% of the total course mark.

The instruction for Assignment 3 have been added to the next post.

Tuesday, 6 May 2014

Downloading species data from GBIF for Friday 9 May

You must download the data for your invasive species from the GBIF portal by Friday 9 May 2014


We will review your attempts on Friday when we will start to look at cleaning your data.

Compulsory reading for Friday 9 May

You must read the following three papers by Friday 9 May

: An assessment of zoological research collections in South Africa
Research and Societal Benefits of the Global Biodiversity Information Facility: http://www.bioone.org/doi/pdf/10.1641/0006-3568%282004%29054%5B0486%3ARASBOT%5D2.0.CO%3B2

Interoperability of Biodiversity Databases: Biodiversity Information on Every Desktop

How Global Is the Global Biodiversity Information Facility?

Principles of data quality

Monday, 5 May 2014

Biodiversity data resources and data quality

On Tuesday 6 May we will be covering the following topics, please take a look at these resources:

Introduction to biological collections 
Biodiversity data resources
Storing data digitally
Spatial versus attribute data
Assessing data quality

You will be expected to work through these resources thoroughly on your own after tomorrows discussions

Friday, 2 May 2014

DIVA GIS and environmental niche modelling excersise

You will be using DIVA GIS for the niche modelling of the species you have chosen to investigate its invasive potential.

On Friday 2 May we will be learning how to use DIVA GIS for the climate envelope modelling you will be doing on your species by doing an exercise on modelling the distribution of  wild peanuts.

You should work through the basic DIVA GIS tutorial before our session on your own in order to find the tutorial easier as you will know the programs basics.

After this you should be able to start modelling on your own species data.

Note: we will be helping you with resource etc of where to find data for your species. Keep an eye on this blog and the main BCB Honours BIM blog

BIM Honours Assignments for 2014

Here is the list of assignments which will be expected to complete for this course. The list includes a short description, percentage of the total course mark and  the deadline for each assignment.

Your final and main assignment will be a research paper on the invasive potential of a species of your choice.

You will naturally be getting more information about these assignments and what is expected of you as the course continues.

Assignment 1: Glossary for terms specific to Biodiversity Information Management
10% of total mark
End of the course

Assignment 2: Data Portal review e.g. Landcover.org, Fishbase, Algae base, etc
10% of total mark
Friday end of second week

Assignment 3: Using the Biodiversity GIS Information portal for Landuse Decision Support
10% of total mark
Friday end of third week

Assignment 4: PowerPoint Expert System for your chosen species
10% of total mark
Friday end of fourth week

Assignment 5: Present Research proposal - Species Invasive Potentail
20% of total mark
Friday end of fourth week

Assignment 6: Research paper on the invasive potential of your chosen species
40% of total mark
Friday two weeks after the end of the course

Hi BIM Honours Students

Welcome to the BIM Honours Blog 2014.

On this blog we will put up notification of what we expect you will be doing and what we expect you to prepare for when we meet.

We will be meeting all day on Tuesday and on Friday afternoons.

Note that many on the posts in this blog will refer to the main BIM Honours Blog which you can regard as a general course resource while this blog will contain the details and dates specific to 2014.

You can find the main BIM Honours Blog here bcbhonoursbim.blogspot.com

In the next few post I will put up details of what you must prepare for Friday 2 May and Tuesday 6 May as well as the details for your assignments.