NUANCE – August 2014

Zimbabwe launches NREN

 A National Research and Education Network (NREN) is born South of the Sahara. Launched on August 7, 2014, at Midlands State University in Gweru, Zimbabwe, Zimbabwe Research and Education Network becomes the 15th NREN in the region.

Speaking when he handed over the certificates of registration to Professor Edias Mwenje, Acting Chairperson of Zimbabwe Universities Vice Chancellors’ Association, (ZUVCA), Professor Ngwabi Bhebe one of the champions for the NREN in Zimbabwe,  indicated that the formation of ZIMREN was inevitable considering that Zimbabwe’s central location entails that the research and education backbone links from the rest of the region pass  through the country.

He further indicated that Zimbabwe was ready to work hand in hand with the rest of the regional players in fostering development of research and education and that the nation through ZIMREN was also ready to tap into the benefits of the AfricaConnect project which is rolling out the regional component of the high speed backbone network for research and education, the UbuntuNet.

Professor Bhebe also expressed gratitude to the UbuntuNet Alliance for supporting and guiding the formation of ZIMREN.
Speaking on behalf of UbuntuNet Alliance, Communications Officer for the Alliance, Patricia Mtungila welcomed ZIMREN into the research and education arena and urged the new NREN to swiftly take its steps into formally joining the Alliance and indeed the  AfricaConnect Project.

UbuntuNet Alliance is the regional Research and Education Network for Eastern and Southern Africa working with established and emerging NRENs to enable collaboration in research and education over world class networks, and has the primary responsibility for the regional research and education data network, UbuntuNet.The UbuntuNet network has seen countries like Kenya, Uganda and Zambia enjoying tremendously low connectivity costs for their research and education institutions.

Eastern and Southern Africa alert on Ebola

 As research into finding a cure for the deadly Ebola virus continues, the World Health Organisation (WHO) has approved the use of untested Ebola drugs to treat the current outbreak in West Africa.  The move has sparked a debate among medical ethicists but international media  reports that the WHO said at a news conference in Geneva on Tuesday August 12, 2014 that the use of untested drugs was ethical, provided certain conditions were met.

The experimental treatment is the same that was used to treat two Americans and a Spanish priest, who contracted Ebola in Liberia.  Sadly, the priest had died but the other two patients are said to be improving.

The virus, spread by direct contact with bodily fluids was detected in Guinea in March and has since spread to Sierra Leone, Liberia and Nigeria. An estimated 1000 people have died from Ebola virus disease since.

In a collaborative approach, Ministers of Health from Southern Africa met early August, to discuss ways of preventing, but also tackling Ebola, should the region have to face the virus.

But efforts against Ebola started sometime back in Eastern and Southern Africa. Uganda lost a doctor in June who got infected while in Liberia where he was working. The country has since engaged in intensive civic education campaigns.
In Malawi, Government through the Ministry of Health issued an alert at the beginning of August aimed at reassuring citizens that the disease was not in the country and also to list the symptoms of the disease.

As for South Africa, SABC TV indicates that a directive has already been issued for people coming from high risk countries to be screened at airports.

The Zimbabwe government has been upbeat about raising awareness on Ebola and ordinary Zimbabweans are now knowledgeable on the virus.

“Actually here in Zimbabwe we are alert on Ebola, I have been reading about it on the internet just to see if it is anywhere near our neighbours,” said Takudzwa Musonza, a waiter at one of the restaurants in Harare.

The WHO website lists the signs and symptoms of Ebola as a severe acute viral illness that is often characterized by the sudden onset of fever, intense weakness, muscle pain, headache and sore throat.  WHO adds that these symptoms are followed by vomiting, diarrhoea, rash, impaired kidney and liver function, and in some cases, both internal and external bleeding. Laboratory findings include low white blood cell and platelet counts and elevated liver.

As the fight against the Ebola virus rages on perhaps NRENs can play a critical role in facilitating collaboration and sharing of information. Already, a wealth of information on research on the virus is there and can be accessed through the AfricaGrid Science Gateway’s Clinical Trials Database.

NSRC, INASP fellowships to recognize pioneering engineers

Over the years many young engineers from Eastern and Southern Africa have benefitted from capacity building programs by UbuntuNet Alliance and its partners. The initiative is implemented through a number of formats including: training of trainers, training workshops; secondment of experts from NRENs with advanced networks to those whose network are under development; and internships.

These Training of Trainers sessions (TOTs) have enabled engineers from emerging NRENs to gain rare skills in among other things advanced routing and managing campus networks.  Engineers who  have gone on to do amazing things in replicating their skills by  training others  now stand a chance to be awarded full travel fellowships to attend UbuntuNet-Connect 2014 in Lusaka, Zambia in November this year.

The capacity building program is a partnership between the Network Startup Resource Center (NSRC), the International Network for the Availability of Scientific Publications (INASP), the Internet Society (ISOC), the Association of African Universities (AAU) and the AfricaConnect project.

According to Steve Huter, Director of NSRC, the NRSC Engineering Fellowships will enable five outstanding engineers to enjoy sponsorship worth US$1,250 each to attend the two-day conference in the Zambian Capital of Lusaka.

Meanwhile INASP has also allocated $7500 dollars for star performing engineers who from Tanzania, Uganda and Zambia to participate in the UbuntuNet Alliance annual conference as “INASP Engineering Fellows” also to the tune of $1250 per person.  Awardees of both Fellowships will be selected through a very competitive process which is being developed and will be announced in due course.

The UbuntuNet-Connect series of conferences has been held for the past six years and is one of the premier conferences in Africa. This year the conference, themed Infrastructure, Innovation, Inclusion, will take place from 13 to 14 November in Zambia, hosted by ZAMREN, the Zambian NREN.

Online Education will democratise and disrupt global learning, IFLA

study predicts that there will be a rapid increase in online resources that will make learning opportunities more abundant, cheaper and more accessible.
Among five trends predicated by the International Federation of Library Associations and Institutions (IFLA) Trend Report, Africa like the rest of the world will see increased value being put on life-long learning and more recognition of non formal and informal learning.Online Open Education Resources (OER), adaptive teaching technologies, Massive Open Online Courses (MOOCS) and gamified learning approaches are expected to transform the global learning landscape over the next decade.
“Digital opportunities for lifelong learning become increasingly essential in amore globalised economy and a rapidly changing technological environment where more people gain new skills and knowledge throughout their adult life,” says the IFLA Report.

The report was presented at the XXI Standing Conference of Eastern, Central and Southern Africa Library and Information Associations (SCECSAL XXI)  conference, a meeting of librarians, information managers and other stakeholders from Eastern and Southern Africa held in Lilongwe, Malawi from July 28, to August 1, 2014.

In a discussion, that followed, facilitated by Buhle Mbambo-Thata, participant Justin Chisenga who is Knowledge and Information Officer at FAO’s regional Office in Uganda said MOOCs and OERs had great potential for Africans and that librarians had a role to facilitate access to these resources.

“Libraries, especially public and community libraries and information centres could play an important role of providing necessary infrastructure for citizens to access and use MOOCS,” recommended Chisenga.

Other members of the panel informing the African discussion of the IFLA Report included Jacinta Were of University of Nairobi Library, Sarah Kaddu of National Library of Uganda and Ujala Satgoor President of the Library and Information Association of South Africa, The IFLA report is also available on while input from the  African discussion has been distributed to SCECSAL members.

African science journalists set to discuss gap with policymakers in Nairobi

By MESHA Secretariat

For the second time in as many years, African science journalists will converge in Kenya on 13 October 2014 to discuss how the gap between science journalists and policy makers can be bridged.

But how did this begin? In August 2012, Kenya’s Media for Environment, Science, Health and Agriculture (MESHA) hosted the first Africa-wide conference of science journalists in the dusty Nakuru town.

The Conference brought together journalists, communicators, scientists and policymakers. During the conference, it was apparent that a gap exists between science journalists, communication officers and policy makers.

In the past there was poor interaction between scientists and journalists, efforts over the past decade, the Conference heard and demonstrated, had seen a warmer relationship emerge. However, policy makers remain less involved in the role played by journalists to bring out science issues especially on rural development and among the urban poor. There was therefore need to strengthen the capacity for reporting on science and technology and promote networking among journalists, scientists and policy makers.

Following the successful 2012 conference, the participants, 180 in number, tasked MESHA to organise a follow up conference with an agenda geared towards challenging policy makers to support the growth of science. During the last Conference, it was also observed that, while policymakers are critical in developing policies to govern science, often they do not factor the responses and needs of the public; a role that media has played effectively.

While this is a very important event on the calendar of science journalism in Africa to and the fledgling science media network in Kenya, MESHA, the organisers of the 2014 Conference recognise the need to tailor make it to have an impactful outcome to the over 100 journalists who will attend as well as reaching another large number who will follow the event through regular updates on line, through media reports, daily conference bulletin and media outlets.

The 2014 conference will launch policy forums and channels with the aim of promoting growth of science that targets environment, health, agriculture and technology journalists, research institutions, civil society organisations, universities and policy makers. It will challenge stakeholders to move beyond conference and government declarations to tracking progress through science journalism. The Conference provides an opportunity through a follow up mechanism instituted at MESHA to ensure that capacity for developing regular impactful interactions and networking among scientists, policymakers and science journalists is instituted in a logical and structured manner.

According the chairperson of MESHA, Ms Violet Otindo of K24, the conference provides a platform where journalists, policymakers and scientists can freely engage on how to push science high in the development agenda of African countries.

“This is not a conference of talk and talk. It is an avenue of linking up with what scientists are doing within the communities,” said Aghan Daniel, MESHA Secretary.

He added that the organisers have line up exciting field trips to confined field trials for genetically modified maize and to a centralized double haploid (DH) facility expected to produce at least 100,000 DH lines per year by 2016, thus strengthening maize breeding programs in Africa and improving breeding efficiency. The DH technology aims to reduce the cost and time for breeding work as it enables rapid development of homozygous maize lines and fast-tracking development and release of elite maize varieties.

Journalists will have first-hand experience with how communities are adapting to climate change to how simple tissue culture technology has changed the lives of small scale farmers ten years on.

SoyKB and iPlant streamline complex bioinformatics analysis

Even though next-generation sequencing (NGS) — with millions or billions of DNA nucleotides sequenced in parallel — is much less costly compared to first-generation sequencing, it still remains too expensive for many labs. NGS platform start-up costs can easily surpass hundreds of thousands of dollars, and individual sequencing reactions can cost thousands per genome.

To garner accurate information, the data analysis can be time-consuming and require special knowledge of bioinformatics. Even so, this high-throughput computational analysis is the backbone of novel discoveries in the life sciences, as well as in other domains including anthropology, social sciences, and plant sciences.

“Using next-generation sequencing you’re getting a snapshot of everything that is happening in a given genome up to that point,” says Trupti Joshi, assistant research professor in computer science and core faculty at the Informatics Institute at the University of Missouri (MU), Columbia, US.

Joshi manages SoyKB (Soybean Knowledge Base), a free online data resource infrastructure that was developed as part of the Obama administration’s $200 million Big Data Research and Development Initiative. Joshi’s team is working with the iPlant Collaborative and XSEDE (Extreme Science and Engineering Discovery Environment) teams to integrate SoyKB data resources and analysis tools.

In addition to integrating SoyKB — which already includes many built-in informatics tools — with existing iPlant tools, the MU team is developing additional toolsets that will also be available to the iPlant community. “Right now we are building the infrastructure so that we can submit jobs — RNA-seq analysis is just one example — to iPlant Atmosphere.” Joshi says three to four different analysis capabilities will be available in a couple months.

SoyKB includes the tens of thousands of genes in the soybean genome, experimental data related to gene expressions, fast-neutron mutation data, and soybean lines GWAS (genome-wide association studies) data. SoyKB is unique in that it includes ‘multi-omics’ experimental data that might otherwise be irrelevant (thrown out) by a particular researcher at a particular time. By making all research data available, experiments take on an increasingly important role in the bigger picture, and enable future researchers to narrow their own results.

iPlant includes storage resources for large datasets, high-performance and cloud computing services to analyze and solve complex research problems including genome assembly, annotation, and association studies. Video courtesy iPlant Collaborative.

Researchers may want to look at soybeans that have a high-oil content, for example, or a high-protein content. Or, they may want to focus on soybean lines that are more drought, disease, or insect resistant. Scientists can access data on particular genomic variations directly in SoyKB, using tools to quickly query and isolate items of interest.

“One of the biggest advantages here is that iPlant is an integrated environment,” says Mats Rynge, who is part of XSEDE’s Extended Collaborative Support Service Workflow Community Applications team. “The iPlant team clearly understands the science and can tailor their services and setup to a biologist.”

More than 19,000 users take part in the iPlant Collaborative, and about 2,500 of them use Atmosphere — iPlant’s cloud service that is fully integrated with user management and the Data Store (570 terabytes). “Atmosphere is one of the nicest academic cloud implementations available,” says Rynge. “I would say it is on par with Amazon in terms of user interface; really well done.”

Rynge is developing a SoyKB submit infrastructure and Pegasus workflows for scientists to pull data from the data store, analyze it, and deposit the results back in the data store — all with the click of a button. The ultimate goal is to make the workflows general enough to be mapped to other infrastructures, which future sequencing groups can use as a starting point.
As NGS techniques continue to amass more data than labs and researchers can handle on their own, high-performance computing and infrastructures capable of presenting, analyzing, and storing data will remain critical resources for complex bioinformatics analysis. After all, with 50,000 to 70,000 genes in a single soybean, looking at thousands of soybean genomes can produce several gigabytes of data for each soybean line.The progress of SoyKB as part of the Big Data Initiative was presented at the IEEE International Conference on Bioinformatics and Biomedicine, December 2013, in Shanghai, China. The US National Science Foundation funds the ongoing project.

First published in ISGTW on August 13, 2014

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