Wednesday, 4 November 2009

IDRN conference - Review

A review of yesterdays conference on health mapping will give you some insight on the current state of mapping practice in health research and related areas. The day overall was interesting and my poster presentation went well, there were some interesting discussions. The city migration behavior of individuals seemed interesting for health researchers. However the day was packed with talks and that was the main bit.

The first speaker will be Dr Russell Stothard from the Natural History Museum. He is talking about the use of GPS. His talk has the title ‘Using GPS/GIS for Schistosomiasis research - building a better picture of exposure to water contact sites’.
First he is pointing out that actually it is possible to geotag an image. Well this is a start. He introduces us to handheld devices available to time and location stamp data such as images. This probably sets the context of the conference. It is a different field than we are used to. He goes on about the GPS system on how global positioning works. He is working in Africa and this might give a different setting. However somehow I get the feeling that there is still a mystical aura to the continent, you could maybe still get lost down there. He moves on to talk us through the Garmin devices available and there he mentions a nice expression for the back tracking setting, Bread-crumbing. How cool is this. This might lend a new title to the urbanDiary project as we are bread-crumbing across the city.
The fact that there is not a GPS camera at current is presented as very sad, but actually there might be software solutions for this?
Interestingly he then starts talking about the location as such and the following slide is titled ‘so precisely knowing where things are has never been easier’. Furthermore he points out that actually the location might not be the actual site of where something is, so to say location is not location.
He show some of the examples he is working on. It is about a disease in Africa that is using a snail as a host. He is working on the East coast of South Africa. Snail species are quite difficult to tell apart, and the disease is picky, living only in one type of snails. So they have to go out and collect the snails take them back to the laboratory to determine what species it is. The location information therefore is important to reconnect the sample with the area of collection. It is a lot about mapping the source (snails) and the impact of the disease. Part of their conclusion then is that the spatial distance from the water source, where the snail hosts live, results in a higher possibility of having the infection. Largely the research is about the lifecycle of the disease.
He also shows a nice device iGotU. This device was used to track 20 people of a village. They are tracking the people to determine the amount of risk they are exposed to. There are also time aspects as there are only certain times of the day where the snails shed to release the larvae to infect people. He shows a timelapse of the peoples movement over a two day period. This tracking determined quite clearly the contact these people have with the water. It is a very nice example for the use of GPS. However the standard questions remain what does that actually say. Is this just a scientific There are the strong cycles these people follow, but somehow these aspects have not yet penetrated the research. If the nail has a cycle and the people have a cycle you can mach these up? There might be a chance to change the peoples habits to prevent them from getting infected. This might not be as simple as they mostly rely on fishing and this in turn requires a naturally determined schedule in order to get a good catch.

Next speaker is David Aanensen from the Imperial College London talking about ‘ - tools for mapping infectious disease epidemiology’. Introducing us to Google Maps use in health research. He also points out there are other services including OSM. So Mash-Ups are the hot key word. He introduces a series of mashups that he has worked on mapping gene sequences, if I have understood him right. He is talking rather casually. The live demo of his websites makes him rather nervous, surprisingly. But it worked well and he was able to demonstrate how it works comparing a set of genes across different countries, by a manual selection done in the mashup.
The big question with thee mash-ups probably really is the accessibility for further research. It is mainly a visualisations the public world wide web, but what now. How can other researcher collaborate or use the provided data? It looks nice but the usability is not yet clear. Do the for example offer an API, for other people to access the data and mash it up? He then shows an other example that to some extend partially answers the question. A platform that can be accessed to produce maps. It is based on a copy past eel data input field to import data and map it.
He moves on to demonstrate a mobile device application he has developed. Especially for the android. The app does allow to input data, adding GPS location and sync is with a web server. Also directly mapping it on a map. It additionally allows for pulling data from the server to see the new records in context or deciding on where to collect more data. He summarizes the limitations of the technologies. The big problem is the battery live, but also the network coverage and the costs, both for the handset and the contract.
He mentions in the end that they have actually just release an iPhone app - lets check EpiCollect on the app store. Haven’t been able to find it so far.

It follows Dr Mat Fisher again from Imperial College London. His talk is entitled ‘Using Google Earth to identify populations and invasions in emerging fungal infections’.
He uses the mapping to predict and an link it to analysis, pattern and process. He stresses that the mapping does not tell us anything unless we have a clear design of the research of what to get out. He shows a clear example of spatial spread of a disease in southern middle America over time. Spreading from 1987 from Costa Rica to Panama City in 2008. So he then uses global mapping based on Google Maps to ma the other occurrence of the disease on this scale. This makes a lot of sense if you can combine it with other environmental data available globally, such as whether and climate data.
Identifying potentially vulnerable locations is very important as the disease is highly spreadable and deadly for amphibians. He provides an example of the extinction of the ‘Spring from that happened this year after the introduction of the disease in March 2009, and by now he frog is belied to be extinct. The protection of these identified areas with similar condition is key.
He shows an example of his work hunting frogs across Europe. For the data storage he is in fact using Google docs. He is even using the KML function provided by the Google Docs. Even though it is limited to some four hundred examples.
The output is clearly spatial. However this could have been expected as for one he is collecting spatial data and for two animal habitat are spatial determined by conditions. To verify the spatial data he is using the barcode technique. They go ahead and determine the gene of the infection and can show that they are locally connected and individually introduced.
So the result shows that the infection is related to UVB, min. temperature and longitude.
In an additional example he shows time based location data of samples from the UK and visualises the spread of a virus in amphibians across the UK from 2001 to 2008.

After the coffee brake speaks Dr Marianne Sinka and Mr Will Temperley, University of Oxford about ‘Mapping the geographical distribution of the Anopheles vectors’.
What are the aspect of mapping malaria data are producing predictable global distribution together with a summary of bionomics, as well as compare the data. She explains how the initial database of vector transitory animals is generated form existing publication sources. Basically she has subscribed to any malaria related publication source by email and gets news to put directly into the data base if related to animal species samples and locations of those. Additionally they add spatial information to the database. Together with a group of experts with detailed knowledge of the locations they have produced area coverage maps.
In terms of technology they are using PostgreSQL data base, combining excel and shape files. Accessing the database is via Python. For the web based stuff they are using Django and Python, but are now developing a Java an Google tool kit based version because of the demand on dynamic content.
Together with spatial, physical data I suppose, and climate data they can model potential areas where a certain species can be found, As a result they are aiming at publishing papers this year on the first set of maps.

Talk by Dr Richard Myers, Health Protection Agency Centre for Infections with the title ‘ Web based GIS mapping of molecular / epidemiological database. They are working on Swine Flu, TB an so on. He runs us through the functional diagram of his functional database. Data Input - Data Storage- User Interface - Data Retrieval and Data Analysis.
For his talk he identified a set of three areas that are important to be looked at to produce a good web based mapping application. The most important aspect he stresses is the why and what you want to get out of the mapping exercise, as the web based formation has its limitations. The two other ones are data and sampling also in terms of the reliability of the data. Interestingly he points out the identification problem with small scale data. They are working with postcode level data. On this level individuals can not be identified , but the zoom factor is important, as they don’t want to have individuals identified in a location.
For the website application they are using flash for the visualisation. It looks nice but he points out some downsides to it. It is slow and currently low resolution as well as limited capacity to show multiple data sets.
So he moves on to show examples of Google Maps. His list o pros and cons of using Google Maps for the mapping is rather long on the other hand. The surprising result is the slowness of it that he points out.
What cannot be displayed on web enable databases. He concludes with a list containing, confidentiality data, dynamic data, local out brakes, detailed analysis and so on. And the list of what is possible is as long, most technological based here though.

Navigation through London comes after lunch presentation it is Tim Fendley, Applied Information Group from Legible London – a way finding system for London. He starts with an introduction to navigating London with some hilarious examples of guidance through the city. He continuous with the examples of psychogeography and the urban islands.
It is for a change a really refreshing talk with a lot of energy and joke. It points out how dry and dull the rest of the day was.
He then runs us through how they have developed and introduces the new navigation elements. The structure for the new navigation system is all based on the naming of locations. There is also a very detailed process to actually develop the maps and navigation aids. Defining the named areas is tricky and a statement of position. The whole system appears very much connected to the tube stations, as it seems to mainly address the tourists and visitors. It is true that the tube is a simple way to navigate London and building on this is one way of tackling the problem. But I think it still has to proof its use for local people. However as they focus at the moment on central London most people going around there are in fact visitors. It will be interesting if this gets rolled out over London and how people learn to navigate their neighborhood.

Chris Phillips of MapAction is talking about, would you guess it, ‘Maps in Action’. Subtitle ‘Disaster mapping at the front lines’. They are working with a rapid responds mapping team. They get deployed within hours of a disaster to the location. They claims to be local within 24 hours. From the equipment box: laptop, GIS, Google Maps/Earth, printer, GPS and camera. There is actually an UN respond team, but it takes them about 4 to five days to get their container shipped into the area.
They are working all over the world and the work is obviously very much appreciated by locals suffering from the event. Usually afterwards they are hired to train locals for continuing the job and to prepare for an similar event. He points out the importance of spatial information in struck areas beside all the equipment. And he mainly draws o the visual aspect of the information and these implicitly to understand the information as compared to text information. The title is interesting - ‘everything happens somewhere’ - as a justification of his work, but it might be also his philosophy. He draws on the aspect of solving the chaos. He also points to some volunteer mapping project like john the map cartographer - mapping towns on his bicycle. Actually this was a promotion talk for mapping, concluding with everyone can map and everyone should map actually.

Peter Yang & Tian-Wei Sheu, National Taichung University, Taiwan with ‘An Effective Use of Social Network Analysis for the Study of Taiwanese Employees' Mental Health at Work’.
He is focusing on the social network analysis and the aspects of health. The term social capital seems relevant, but hard to define. His use of the analysis is rather focused on networks. He identified five types. Dispersion, Durability, homogeneity, intensity and reciprocity. To get the data he used questionnaires. For the analysis he is using the UCINET 5 for Windows. However the important finding here is probably that location information is not only about maps, but also about networks and connections, crossing points and so on.

The last presentation for the conference is given by Dr Mikaela Keller, Harvard Medical School, USA on ‘Mapping the influenza A H1N1 outbreak’. Unfortunately my macBook run out of battery and I had a chance to follow her talk in more detail. To take it up front she also showed a iPhone application for the project she is working on. It is available on iTunes and simply called heathMap. This is at the same time the project in short, mapping news of diseases. They have invented a internet crawler that works on the basis of text and sentence structure recognition to spot any news in the text, grabbing location and disease transferring it into the database and producing Google Maps mashup with the data. This information is then accessible to the general public. However this is where the critique on the system pulls in. What is the benefit of the information to the general public. And who exactly is this ‘general public’. It goes a step further, as the presented iPhone application actually allows the ‘general public’ to directly submit a ‘case’, including disease (from a suggestive pull down menu that tells you up front it must be swine flu) and location of course. You can even include an photograph of the sick person if you’d like to make a point! I find this very doggy even though the project as a whole has some very interesting aspects. For example the idea of looking at the world as a whole and visualising everyone on the planet as part of the whole.

Somehow I have a creeping feeling that some of this research somehow still has a colonial aspect to it. It is interesting to look into problems of distant locations as some sort of export, but not as working together.
Also all this spatial mapping is pointing towards the time-space problem and the issue with location information. It is in fact tied to the idea of the globe (as in the globe on your desk as a rotating ball on a axis that represents an abstraction of the world) and if this view is outdate the visualisations are too. So what to do? Is the mapping guild in a crisis because everyone is mapping? All this here seems to be riding on the open source mapping wave.

This question is urgent and regarding the take I went to in the evening at the Tate Britain by Doreen Massey a debate around these subjects is ongoing and the question of place and identity are up for challenge, but have to be redefined in the globalised world. I strongly agree with her view on the importance of boundaries for the structuring of places and especially with the argument regarding the human body as the first place it seems obvious to have a definition of the self and the other. And if it is something, it is not something else and this makes the distinction between the two. The main aspect is the way boundaries are set up and maintained in terms of the political dimension.

No comments: