The fourth paradigm: Data-intensive scientific discovery

This book by Microsoft Research argues that "scientific breakthroughs will be powered by advanced computing capabilities that help researchers manipulate and explore massive datasets.

The speed at which any given scientific discipline advances will depend on how well its researchers collaborate with one another, and with technologists, in areas of eScience such as databases, workflow management, visualization, and cloud computing technologies."

Read more ...

Scientific data and information increasingly interconnected

Timo Hannay in Nature's Nascent Blog:

"Scientific knowledge — indeed, all of human knowledge — is fundamentally connected ... So even as the quantity of data astonishingly balloons before us, we must not overlook an even more significant development that demands our recognition and support: that the information itself is also becoming more interconnected. One link, tag, or ID at a time, the world’s data are being joined together into a single seething mass that will give us not just one global computer, but also one global database. As befits this role, it will be vast, messy, inconsistent, and confusing. But it will also be of immeasurable value—and a lasting testament to our species and our age."

Information, knowledge and communication in the new CGIAR strategy

The international agricultural research system of the CGIAR is undergoing a large transformation. A recent Progress Report No. 4 "presents interim findings and proposals of the Strategy Team for review and discussion."

The proposed 'Strategy and Results Framework' introduces seven interlinked Mega Programs and two platforms — gender and capacity strengthening - that will serve as the building blocks for the work of the 'new' CGIAR.

How do information, knowledge, ICTs and related areas fare in these proposals?

Mega-Program 3 is titled 'Institutional Innovations, ICTs, and Markets.' Its focus will be on: "Knowledge to inform institutional changes needed for a well-functioning local, national, and global food system that connects small farmers to agricultural value chains through information and communications technologies and facilitates policy and institutional reforms."

This mega program "aims to unleash an ― institutional and information revolution - with and for farmers and the rural poor that improves and secures their livelihoods, and also promotes innovation along value chains." It speculates that the "next big breakthrough in institutional innovation to be unleashed in support of poverty reduction, food and nutrition security, and environmental sustainability" might include: "linking of information and communications technologies (ICTs) to value chains and services for the poor in rural areas, through, for example, the cell phone and its increasing range of sophisticated derivatives."

Within Mega Program 1 on 'Crop Germplasm Conservation, Enhancement, and Use', a program is envisaged to "integrate bioinformatics and crop information systems."

These proposals seem to recognize the importance of knowledge and information as well as ICT applications and tools within both CGIAR research processes and the agricultural nnovation systems where organizations doing research and development interact. Hopefully, it will boost scattered efforts to increase research uptake, interaction and collaboration using ICTs and other innovative approaches to knowledge sharng and communication. It would usefully also emhpasize the potential for co-creation of knowledge and information among the partners.

The cross-cutting 'capacity-building platform' will "strengthen the capacity of the CGIAR and its partners through improved research networks, information technology, knowledge management systems, and training. The expected result is a dynamic knowledge creating and -sharing system comprising CGIAR centers, strong independent national agricultural research systems, and other research partners sharing knowledge."

The capacity strengthening role of the CGIAR is recommeded to "have two purposes: strengthening capacity for all Mega Program partners by fostering research collaboration and networking, and strengthening capacity for weak national agricultural research systems."

"An important element of both activities will be the development and use of advances in information and communication technologies (ICTs) and knowledge management and innovation systems, including access of Mega Program partners to applications and resources such as databases."

These proposals seem to include work by CGIAR centers to make their data, information and knowledge accessible (see recent work on AAA and CIARD), so often limited-access knowledge is freed to be exchanged and re-used. Hopefully, they will not forget the importance of open licenses such as creative commons, and open access in general. The 'public goods' need to be made public!

Under a heading 'Communications Strategies,' the document also argues that "research programs have no impact without communications: innovations, research results, policy assessments, and policy recommendations are useless if they are not communicated to those who can use them."

They suggest an 'umbrella communication strategy' that will "make clear what the CGIAR’s vision means in concrete terms and what the new CGIAR will do to achieve its visionary goals."

Each Mega Program will therefore have a "defined communications strategy that outlines the key messages to be conveyed, the key target groups, and the media and channels for communicating with the key target groups." To maximise synergies, "the mega program communications strategies will be coordinated with the umbrella communications strategy for the vision."

Building communications - as well as information access and knowledge sharing - into each Mega Program seems very sensible. Let's hope the designers adopt the DFID Research approach that calls for 30% of a project's funding to be be allocated to communication and uptake.

Access to Research for Development and Innovation - WIPO supports free journal access

The United Nations has partnered with the scientific publishing industry to provide research institutions in least developed countries free access to online journals, the UN World Intellectual Property Organization (WIPO) announced at the launch of the scheme in Geneva.

The new UN-brokered programme, Access to Research for Development and Innovation (aRDi), will allow industrial property offices, universities and research institutes to subscribe free of charge to prominent science and technology publications including the American Institute of Physics, National Academy of Sciences, Oxford University Press and Royal Society of Chemistry, among others.

Read full article.

Maintaining the integrity and accessibility of research data

According to a new report by the National Academy of Science, "maintaining the integrity and accessibility of research data in a rapidly evolving digital age will take the collective efforts of universities and other research institutions, journals, agencies, and individual scientists."

The report recommends that researchers - both publicly and privately funded - make the data and methods underlying their reported results public in a timely manner, except in unusual cases where there is a compelling reason not to do so, such as concern about national security or health privacy. In such cases, researchers should publicly explain why data are being withheld. But the default position should be that data will be shared -- a practice that allows data and conclusions to be verified, contributes to further scientific advances, and allows the development of beneficial goods and services. Research data can be valuable for many years after they are generated -- for verifying results and generating new findings -- but maintaining high-quality and reliable databases can be costly, the report observes.

Read full article

How journal articles may come to be published

"Cell Press and Elsevier have launched a project called Article of the Future that is an ongoing collaboration with the scientific community to redefine how the scientific article is presented online.

The project's goal is to take full advantage of online capabilities, allowing readers individualized entry points and routes through the content, while using the latest advances in visualization techniques. We have developed prototypes for two articles from Cell to demonstrate initial concepts and get feedback from the scientific community."

What do we think? Seems to be more about presentation and the introduction of other types and forms of results (podcasts, video). Doesn't seem to suggest any opening up of all or some parts of the content.

Science blogging: The future of science communication?

The relationships between science journalism, science communication and new social media was one of the discussion points at the recent World Conference of Science Journalists.

A recent post by Daniel D. Brown on his Biochemical Soul blog explains why scientists and science students should follow science blogs:

1. To keep up to date on fascinating research
   
2. Join in the great discussion
   
3. Science blogs allow you to talk about science in an informal setting
   
4. Gain emotional and social support from like-minded people
   

Why they should start a science blog:

1. Share your passion for science
   
2. Be a part of the community
   
3. Make connections
   
4. Be a part of “the good fight”
   
5. Become a better writer
   
6. Hone your ability to distill complex research into understandable terms
   
7. Showcase your dedication to science and your interest in outreach
   
8. Get feedback on your own thoughts and/or research
   
9. Blogs are great teaching tools both inside and outside the classroom
   
10. Increase the visibility of yourself, your lab, your department, and your University
    
11. Have fun

Science communication and science journalism

In London this week, some 900 people have signed up for the 6th world conference of science journalists.

There is a wide range of presentation and discussions - looking at mainstream science communication, journalism, and the use of new media.

As well as the WCSJ news site, an especially good place to follow the discussions is on Twitter – http://twitter.com/#search?q=wcsj

See also the excellent Nature magazine special on science journalism as well as blogs from SciDev.net and by Angela Saini.

ICTs and agricultural science - notes from the Science Forum workshop

Last week's Science Forum in Wageningen included a workshop on information and communication technologies - ICTs. Organized by Ajit Maru from GFAR, Some 50 people joined intense discussions on a broad range of ICTs and their future potential application in agricultural sciences for development.

The overall conclusion of the workshop discussions was presented by workshop facilitator Peter Ballantyne to the Forum plenary on the Wednesday afternoon:

"Much more participatory, collaborative, creative and ‘impactful’ agricultural science and innovation is possible by investing in ‘ICTs.’ Not just for the scientists, but along the ‘chains’ of producers, traders, and consumers."
Some other 'bullet points' from the presentation:

The trends - or waves - of the ICT world likely to positively impact us in the future include:

• Pervasive low-cost and mobile connectivity, across many different devices and platforms, reaching far beyond traditional research communities;
  


• Exponentially growing processing power, allowing complex problems and large data sets to beunderstood and handled; 
  


• 'Clouds' of shareable tools, applications, and intelligently-linked content and data, putting massive storage and sophisticated tools within the reach of all; 
  


• Growing capabilities to collect, analyze and re-use massive distributed collections of data, opening up new possibilities to carry out science across borders;
  


• People and ‘crowds’ empowered to create and manage data and information, allowing the multiple knowledges of different people to be mobilized. 
  

Full details from the group discussions will be brought together with the background paper, thinkpieces and the summary presentations into a report.

See materials from the workshop on the GFAR web site.

by Peter Ballantyne

Communicating swine flu research - Evidence for open access models?

Through Twitter, just came across fascinating blog post from leading science writer and blogger Carl Zimmer...

In his posting, he describes his positive experiences trying to obtain information on swine flu science.

Concluding that "the patient process of old-fashioned science publishing may have to be upgraded", he show how scientists working on the virus created an open wiki (thanks to them for the image on this posting) to share information - "So everyone who wanted to peruse their analysis could see how it developed as more data emerged and as they used different methods to analyze it."

After this open process, it seems the results were published (today 11 June) in Nature - with a Creative Commons license.

Of course, this openness may be due to the urgent nature of the problem. But it does show a different - and open - way to do science. This model combines open 'social' media like wikis and blogs with publishing in a traditional peer-reviewed journal, and the use of creative commons licenses to maximise access to the results.

It sounds like several of the promising pathways CIARD aims to pull together to make agricultural research outputs more accessible!

Social media for agricultural science?

Looking back on 20 years of the world wide web, the Economist reports on the original "bland title' of a document written by Tim Berners-Lee in March 1989: "Information Management: A Proposal." It argues that "his proposal, modestly dubbed the world wide web, has fulfilled the implications of its name beyond the wildest dreams of anyone involved at the time."

The short article illustrates ways that scientists are "using the web to further their research." However, it suggests that scientists have "tended to lag when it comes to employing the latest web-based social-networking tools to open up scientific discourse and encourage more effective collaboration."

"Scientists publish, in part, because their careers depend on it. They keenly keep track of how many papers they have had accepted, the reputations of the journals they appear in and how many times each article is cited by their peers, as measures of the impact of their research. These numbers can readily be put in a curriculum vitae to impress others.

By contrast, no one yet knows how to measure the impact of a blog post or the sharing of a good idea with another researcher in some collaborative web-based workspace."

CIAT's Simone Staiger recently shared a presentation to colleagues on the Potential of Social Media for Improving Organizational, Project and Personal Impact in an agricultural research institute. She invites them to join the social web, to increase their 'impact pathways' by increasing their networks and reaching out to more users.

Such social approaches were one of the features of the recent Rome sharefair; they were also used to report on IAALD's 2008 World Congress.

They are thus spreading among agricultural information, knowledge and communication people. However, demonstrating the personal and professional 'business case' for social media in science is going to be an important step towards wide adoption of these approaches and tools.

Making the web work for science

Last week's posting on making our information accessible was picked up by Peter Suber's open access blog.

One of the ways we can make our information and data more accessible is by paying attention to the way we license our content. Over at the Science Commons - a sister initiative to Creative Commons - they are proposing some ways that scientific research can be made “re-useful” — so others can use it in new ways.

View this video on the science commons by Jesse Dylan, director of the “Yes We Can” Barack Obama campaign video with musical artist will.i.am from the Black Eyed Peas:

Click to play

See more Creative Commons videos

Ways to blog ...

In a post 'Science blogging is the new email', one participant in the Science Blogging 2008 conference in London gives a really interesting categorisation of blogging:

• conference blogging (also includes event blogging)
• edublogging
• metablogging (blogging about blogging, by far the largest discipline)
• research blogging (blogging about scientific experiments, the smallest discipline)
• investigational blogging
• evolution blogging (a large subdiscipline)
• news blogging (blogging about science news)
• watercooler blogging (small pieces of interesting or funny thoughts/pictures)
• summary blogging (summarizing other blog posts and linking to them)
• diary blogging (blogging as a personal diary of self-expression)
• hoax blogging

It would be interesting to see if we have other types of blogging in agriculture...

Examples of conference blogging are the recent AFITA-IAALD-WCCA Japan congress where we listed ways to access some content and stories from the congress. Another is the series of Brussels Briefings on ACP-EU rural development, where blog stories are combined with short video interviews.

Anyone got examples of other types of blogging ...?

Science blogging to publish research?

The September 18 issue of 'The Economist' has a short article on user-generated science.

It looks at emerging web 2.0 tools in science, particularly blogging, that may lead to news ways to publish and communicate science and research. It concludes that there's much action and progress in the science blogosphere, but: "in order that blogging can become a respected academic medium it needs to be recognised by the upper echelons of the scientific establishment."

It links to Nature Network - a 'professional networking website for scientists around the world', where you can find a information about the recent Science Blogging 2008 conference in London.

The conference ended with a call to get senior scientists blogging. This may be a good step towards recognition that publishing is about more than just academic articles...

Science dissemination with open access

The Science Dissemination Unit of the Abdus Salam International Centre for Theoretical Physics just published a 'compendium of selected literature on Open Access in scientific communication.

The report, as can be seen in the embedded image below, is as interesting for its online format as it is for its content.

open the publication

The publishing platform is called Issuu. According to its blurb, it is "the place for online publications: Magazines, catalogs, documents, and stuff you'd normally find on print. It's the place where YOU become the publisher: Upload a document, it's fast, easy, and totally FREE. Join a living library, where anyone finds publications about anything and share them with friends."

Improving research data sharing and management

The UK's Research Information Network (RIN) just published a report on a project to investigate the publication and quality assurance of research data. The report 'To Share or not to Share: Publication and Quality Assurance of Research Data Outputs', finds that realising the full potential of data requires further progress in data management policies and practice.

The report argues that "research findings in digital form can [nowadays] be easily moved around, duplicated, handed to others, worked on with new tools, merged with other data, divided up in new ways, stored in vast volumes and manipulated by supercomputers if their nature so demands. There is now widespread recognition that data are a valuable long-term resource and that sharing them and making them publicly-available is essential if their potential value is to be realised."

Based on its survey of scientists, the report highlights "two essential reasons for making research data publicly-available: first, to make them part of the scholarly record that can be validated and tested; second, so that they can be re-used by others in new research."

A set of conclusions and recommendations are provided under the headings:

Creating and caring for data

Policy-makers need to take full account of the different kinds of research data researchers produce, the different values they have, and the different needs of researchers and other potential users.

There is a need for co-operation between researchers, funders and institutions to ensure that sustainable arrangements are in place to preserve valuable data and to make them accessible.

Publishing data: motivations and constraints

Research funders and institutions should actively promote data publishing and re-use, with measures including career-related rewards to researchers who publish high-quality data, case studies on the benefits of doing so, support for researchers in developing sound data management plans, and strategies to address current skills gaps.

Discovery, access and usability of datasets

There is scope for publishers to promote ease of access and use of relevant data sets, and a need to clarify the current confusion over policies on access for text-mining tools. The take-up of Web 2.0 applications should be monitored and its implications considered.

Quality assurance

There is a need for further work on acceptable approaches to the formal assessment of datasets across the disciplinary spectrum.

Learning to communicate science

The Australian Centre for International Agricultural Research just published a training manual entitled 'communicating science.' While it misses an introduction explaining its purpose and use, the manual starts by asking 'Why scientists should communicate? what is scientific writing? and why scientists must write?

The core of the manual is a series of modules that explain how to structure and present scientific information, as a report or article, also in a presentation. Each module contains questions and a quick reference guide to the main points covered.

Under 'structure, it introduces titles and abstracts - writing titles that give them impact; literature reviews, paraphrasing and citation, materials and methods, results, and the discussion/conclusion of an article. The final module provides trainees "with a method for overcoming any fear of starting to write and to maximise the efficiency of the writing process."

Tags: agricultural information communication aciar science

BioMed Central launches Open Access portal for developing countries

BioMed Central, the world's largest publisher of open access scientific research, today announced a new information portal calling attention to the developing world's need for open access to the scientific and medical literature. The Open Access and the Developing World portal highlights the most relevant peer-reviewed research from BioMed Central's open access journals and brings together the latest news and resources relating to open access and the developing world.

Tags: agricultural information open access science

Open Access and the Progress of Science

In the May-June 2007 issue of American Scientist, Alma Swan asks if open access can advance science? She argues that the answer is yes, and that the "advance of science is the prime reason that access is an imperative." Further, "open access can advance science and will do so more and more effectively as more scientists make their work freely available."

How to do this? While open-access journals are a valuable option, Swan argues that the "simple alternative" are "robust research repositories." To provide open access, "all that is needed is for each scientist to place a copy of each article, as soon as it has been peer-reviewed, into an open repository at his institution. Known as self-archiving, this act takes a few minutes and costs a scientist nothing."

"By self-archiving, a scientist can banish the threat of that bane of scientific life—obscurity. A few minutes at the keyboard today makes one's work visible to any scientist who might build on it tomorrow. While commercial publishers, scientific societies and librarians struggle over business models and tough longer-term issues such as who will maintain the record of science in a digital age, it remains the individual investigator who has the tools at hand to speed science along."

Tags: open access science