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• Martin Dove

  15 March 2007 | 19:14

  Nature networks as a collaborative tool: starting point for a series of posts

  I have been communicating with Matt Brown by email with various ideas, and he suggested that I should paste my various dialogues here. If Nature Network let us have blogs, I could have used these!

  This first post concerns some general principles. A large part of my work is in escience, and I have become very interested in how internet technologies can support collaborations between scientists. We do work on videoconferencing using the Access Grid, for example, and we have done a lot of thinking about how such technologies compare with email and instant messaging for example. This isn’t particularly clever, but at least we are experimenting by trying. We also use wiki tools a lot, and this brings us into Web 2.0 stuff. I think that some aspects of wikis are brilliant. We started using them quite soon after they come onto the market (I will post about wikis separatelty).

  I learned about social networking via my daughters and members of my research team. My daughters use MySpace a bit, and my team use Facebook. We have had a lot of discussions locally about how social networking could be used by scientists.

  Prior to the release of Nature Network, we had started doing some experiments. We have set up a couple of instances of our own social network system, albeit much less advanced than Nature Network (as you might expect for a couple of people doing it in their spare time!). We even got as far as registering a domain name.

  To illustrate the idea, we recently organised a workshop on the theme of pollutants, in which we brought simulators and field scientists together (link here). In a group of breakout discussions, everyone said the same thing: we need a means by which people in different communities can discover what each other are doing. Some of us who knew about Web 2.0 stuff in each group said something along the lines that we need a MySpace for scientists. (I should interject at this point to note that I don’t know a lot about MySpace because my daughters consider it to be inappropriate for me to join, and I didn’t feel much like being the cyber-equivalent of a stalker, but I did join Facebook and got a little bit of a feel for what that does). Those of us at the workshop agreed that we would attempt to use a social network site to explore whether we could use this sort of technology to help us all learn from each other’s diverse areas of expertise in the field of pollutants.

  So we started to create our own social network for scientists, using two approaches. One based on the elgg framework, and one constructed from scratch using the Django tools. We have got some way along the line, but as you will know, this is all an experiment and requires a lot of thinking as well as programming.

  We have a number of ideas for our vision. Social network as per Facebook is really only part of the picture; my feeling is that by itself it may not end up as much more that “respectable fun” for scientists and science writers. It needs to have the ability for scientists to collaborate, but in a way that enables scientists to also form collaborations.

  Anyways, this sets the scene for the following sequence of posts. I feel that too much in one post will be just that, too much! Hence the sequence.

  Thanks to Toby and Kat for many discussions that are helping to shape these ideas.

• Martin Dove

  15 March 2007 | 19:24

  Blogs

  At the present time, Nature Network has a very restrictive view of blogs. You have to apply to be allowed a blog. In my view this is an absolutely hopeless situation and will limit considerably the value of Nature Network.

  The view at Nature appears to be that a selected group of regular bloggers should be writing for everyone. That is fine for a blogging site, but Nature Network has to be much more than that. Thus I suggest you drop the idea of public bloggers and replace it with the idea that everyone can blog for the benefit of their collaborators, not for the general public.

  I am quite sure that the ability of the people within any community using Nature Network or any similar social network site for scientists to write in a formatted way with embedded graphics (particularly with SVG capability) will be a strong demand. For example, I envisage that any one scientist may want to run several blogs, one per project area that they are involved in, with quite tight access control (eg to groups, or named individuals). Typically in the wider web world, one thinks of people having just one blog with as many readers who might be attracted as possible. But actually many scientists multitasks, and will want to have one blog running that one set of partners can read, and another blog that a different set of partners read. Some blogs may be public, but many will be private.

  My vision of a social network for scientists includes two parts; one is people discovery (eg finding people who have interests and expertise you are interested in), and the other is support for collaboration with people you already know and work with. The first of these involves people “advertising” themselves, partly through their profiles and tags, and their publications, and whatever else leaks through into their public side. The second involves blogs, forums and wikis, each of which fulfils a different function, but which are linked.

  Consider the following real scenario (I think a scenario helps to explain what I mean). I run a small team in Cambridge who are calculating the energies of dioxin molecules adsorbed on clay particles in soils using quantum mechanics. Steve runs a team in Bath but using empirical models. Not only do I coordinate the Cambridge team, I actually coordinate the whole project. So I want to know what both teams are doing. But actually all members of the team want to know what each other is doing, and each member of the team wants to tell each other as well. The view is that close collaboration can lead to much more progress than could be achieved by people working independently. So each team member runs a blog, which is something like a daily diary of what they do – in short the blog becomes the lab-book.

  To add more detail to this scenario, one of Steve’s chaps manages to pull together a set of data which he can plot. All our data is in XML, so using out tools he generates an SVG graph (I will talk about support for SVG later). He puts this onto his latest blog entry with appropriate commentary. All of us involved in the project can immediately read this (and easily find it again to re-read in the following days), and we can all comment and get a discussion going in a way associated with the blog entry. When my person in Cambridge generates a similar graph from her work, she can similarly upload her plot. This time her entry will have a direct link to the blog entry of Steve’s chap so that we can all easily compare the two graphs, and can cross post. The discussion then becomes more general, so we create an entry on our private forum, and start a discussion there. I might then ask a question, for which the answer has to involve another diagram, which somebody puts into an entry on the forum. At some point this work begins to come to a conclusion, and it is appropriate to review the key results. We then turn to the wiki we set up for this project. The wiki originally contained a an outline plan for the work together with links to appropriate publications (including publications by the team members, which are linked from their profile pages). But now we write a commentary on what we have achieved on this wiki, with links to the various (appropriate) blog entries and forum discussions. The commentary can contain the key graphs (which already featured in the blog so a simple link is all that is needed for the graphs to be displayed). Once the work has finished, this commentary is turned into the document that is then published. Access to the blogs, forums and wiki would be restricted to the groups in Cambridge and Bath (and possibly also some other collaborators in UCL who we may want to involve in the discussions); this is controlled by having formed a network/community/group within the social network site. At some point we may think it would be good to talk to a field environmental scientist, and we use a search tool within the social network site to find one or two people who look appropriate. This is based on their subject tags, publications and whatever information the field environmental scientist wants to make available on his/her profile (the social network site will have made creation of this information really easy). The search tool will be able to extract good information out of the publications in fact, so that the field environmental scientist will not necessarily have had to write extensively about him/herself. We then invite the field environmental scientist to join our network/community/group, and explain to him/her that we need their advice. This person is then able to read the commentary of the wiki, and can look back at the blog and forum entries to understand the thought processes that got us to the point. The field environmental scientist then contributes to the forum and the wiki, and in doing the latter becomes a co-author on the paper.

  Meanwhile Steve is running a separate project on the fluid/mineral interface that doesn’t involve Cambridge, so he has a separate network/community/group with other scientists, and a separate set of blogs/wikis/forums.

  Hopefully this explains why I think that we need not only forum capability on a social network site for scientists, but also blogs and forums, and lots of them with finely tuned access controls.

• Martin Dove

  15 March 2007 | 19:33

  Support for SVG graphics

  This is very important. For those who are new to SVG graphics, let me explain.

  Scalable Vector Graphics is a graphics format in which images are represented by lines and fills rather than as bitmaps. This has the real benefit over standard web formats (eg jpg, gif, png) that it really does scale. Bitmap formats have a fixed resolution so if you zoom in to a feature in your plot you end up with the limit that you get blocks of black and white and no new details. On the other hand, with SVG you can scale and scale and always get clean diagrams; and SVG often makes smaller files.

  SVG is an XML format, which means that you can retain information about what you intend the graphics to show, and you can embed additional information.

  Anyways, it is essential that Nature Network has full support for SVG graphics files.

• Martin Dove

  15 March 2007 | 19:41

  Wikis

  As I noted in one of my above posts, Nature Network needs to have a range of tools that provide scientists with the ability to collaborate. For collaboration, I think that the social network site needs to have a significant wiki component, but one has to think about what this means ….

  I use wikis for collaboration in a number of ways. For a project, the wiki provides a means to track work (collaborators edit a wiki page to provide ideas and updates), to write documents collaboratively, to share information (including diagrams and pdf files). In our eMinerals and MaterialsGrid projects, we have all sorts of pages to cover things like tracking and writing papers for conferences, sharing information on collaborative subprojects, writing agendas and minutes of meetings, tracking the progress of collaborative tasks, writing notes on discussions and the like.

  We use wikis in two ways, one to manage collaboration across the project, and second for small subgroups to also manage their collaboration. In several regards this is not really how it should be, in that we shouldn’t really be mixing whole project collaboration with semi-private smaller collaborations. For example, if I want to be updated on changes to the wiki, I shouldn’t have to get updates on the private discussions. These get too entangled. Thus we should be able to define wikis for various different groups of people, and set access limits and alerting information accordingly.

  I also find I am a member of around half a dozen or more wikis, and inevitably I can’t pay attention to them all. It is now the common cry at events where people talk about working together: “we could set up a wiki”. Now I can’t cope with more wikis. Thus I would like all my collaborations to be in one place, with individual access controls per wiki, some being large group and some small group wikis, with alerting from each wiki.

• Martin Dove

  15 March 2007 | 19:43

  Inputting of publication data

  For scientists to share publications is essential. I think that the Nature Network way of adding publications is, I have to say, somewhat too tedious. It may be okay if you have 5 publications and a bit of time, but for established scientists it is too much to have to fill in a form per paper. It would be great if there could be a means by which information and access to publications could be scraped from the internet somehow. There is expertise on this sort of thing. It would be extremely useful if in a minimal number of clicks it would be possible for one person to point a collaborator to one of his/her papers (ie to the journal web site from which it could be downloaded).

• Martin Dove

  15 March 2007 | 19:46

  Nature network as my one-stop shop for collaboration

  I know it is a hated phrase, but it is what I want!

  For example, I could be a member of project-wide groups, but I could also be part of smaller collaborations defined by other private groups. What this needs is the ability to use a mixture of blogging and wiki type tools; blogging to generate discussions, wiki for more democratic work. Both need to be able to upload images of various formats (including SVG), movies/animations and also pdf versions of documents. It actually would also be nice to have something like Google’s office tools available for groups to share, particularly for collaborative writing and data analysis. It would also be nice to have a shared whiteboard with the ability to save in SVG format (I believe the future is XML). And one needs a tunable alerting system that tells me what is new in a way that I want to know about, and in a place on the site that is easy for me to see.

• Martin Dove

  15 March 2007 | 19:50

  Data access

  Collaboration involves sharing data, not just representations of data. A significant part of the vision of Web 2.0 is to be able to take data from various sources and use to create new value.

  I envisage that the social network site for scientists will provide the ability to link to the raw data on our own data servers, with the means to display graphs based on the data. If raw data are in XML format, the web page can display appropriate graphs.

  Thus the social network site will provide a near-complete collaborative environment.

• Martin Dove

  15 March 2007 | 20:00

  Messaging other people

  How about being able to leave messages for people (an alternative to email; one could then add links to content on Nature Network), or running an integrated jabber server for instant messaging? It would be useful to see the status of people you want to talk to (eg logged in). And the ability to leave messages for groups of people as well as for individuals.

• Martin Dove

  15 March 2007 | 20:07

  Discovering people

  Discovering people in Nature Network appears to be awkward and not particularly successful. Searches appear to be on interests, and people interpret interests in various different ways. I have tested this by trying to find one person I know, and to be honest it really is not easy. Well, I can type her name in, but that isn’t the point. I want to search on what techniques she uses, what science she does, what systems she works on etc, but although these are in her tags, there is no obvious way to search on tags. I also want to find other people in my institute, but how to do this doesn’t leap out at me.

• Martin Dove

  15 March 2007 | 20:09

  Internal links

  So I have worked out how to add external links, but why is it that when I want to link to Matt Brown. I have to find the URL and paste this in the formatting. Why can’t I have a means of referring to Matt in some simpler way?

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