Data integration and handling

Modern technology allows researchers to generate data at an ever increasing rate, outpacing the capacity of researchers to analyse it. Developing automated support systems for the collection, management and distribution of information is therefore an important step to reduce error rates and accelerate progress to enable high-quality research based on big data volumes. This thesis encompasses five articles, describing strategies for the creation of technical research platforms, as well as descriptions of the technical platforms themselves. The key conclusion of the thesis is that technical solutions for many issues have been available for a long time. These technical solutions are however overlooked, or simply ignored, if they fail to recognise the social dimensions of the issues they try to solve. The Molecular Methods database is an example of a technically sound but only partially successful solution in regards to social viability. Thousands of researchers have used the website to access protocols, but only a handful have shared their own work on MolMeth. Experiences from the Molecular Methods database and other projects have provided a foundation for studies supporting the development of the eB3Kit The eB3Kit is a portable, robust and scalable informatics platform for structured data management. Deploying the platform enables research groups to carry out advanced research projects with very limited means. With the eB3Kit researchers can integrate data from a wide variety of sources, including the local laboratory information management system and analyse it using the Galaksio interface. Galaksio provides user friendly access to the Galaxy workflow management system and provides eB3Kit users with access to tools developed by a far larger user community than the one actively developing the eB3Kit. Using a workflow management system improves reproducibility and enables bioinformaticians to prepare workflows without directly accessing ethically or commercially sensitive data. Therefore, it is especially well- suited for applications where researchers are worried about privacy and during disease outbreaks where persistent storage and analysis capacity must be established quickly

Galaksio

The Galaksio presentation at the GCC/BOSC 2018 in Portland

Legal & ethical compliance when sharing biospecimen

When obtaining samples from biobanks, resolving ethical and legal concerns is a time-consuming task where researchers need to balance the needs of privacy, trust and scientific progress. The Biobanking and Biomolecular Resources Research Infrastructure-large Prospective Cohorts project has resolved numerous such issues through intense ommunication between involved researchers and experts in its mission to unite large  rospective study sets in Europe. To facilitate efficient communication, it is useful for onexperts to have an at least basic understanding of the regulatory systemformanaging biological samples. Laws regulating research oversight are based on national law and normally share core principles founded on international charters. In interview studies among donors, chief concerns are privacy, efficient sample utilization and access to information generated fromtheir samples. Despite a lack of clear evidence regarding which concern takes precedence, scientific as well as public discourse has largely focused on privacy concerns and the right of donors to control the usage of their samples. It is therefore important to  roactively deal with ethical and legal issues to avoid complications that delay or prevent samples from being accessed. To help biobank professionals avoid making unnecessary mistakes, we have developed this basic primer covering the relationship between ethics and law, the concept of informed consent and considerations for returning findings to donors.B3Afric

Acute hantavirus infection induces galectin-3-binding protein

Hantaviruses are zoonotic viruses that cause life-threatening diseases when transmitted to humans. Severe hantavirus infection is manifested by impairment of renal function, pulmonary oedema and capillary leakage. Both innate and adaptive immune responses contribute to the pathogenesis, but the underlying mechanisms are not fully understood. Here, we showed that galectin-3-binding protein (Gal-3BP) was upregulated as a result of hantavirus infection both in vitro and in vivo. Gal-3BP is a secreted glycoprotein found in human serum, and increased Gal-3BP levels have been reported in chronic viral infections and in several types of cancer. Our in vitro experiments showed that, whilst Vero E6 cells (an African green monkey kidney cell line) constitutively expressed and secreted Gal-3BP, this protein was detected in primary human cells only as a result of hantavirus infection. Analysis of Gal-3BP levels in serum samples of cynomolgus macaques infected experimentally with hantavirus indicated that hantavirus infection induced Gal-3BP also in vivo. Finally, analysis of plasma samples collected from patients hospitalized because of acute hantavirus infection showed higher Gal-3BP levels during the acute than the convalescent phase. Furthermore, the Gal-3BP levels in patients with haemorrhagic fever with renal syndrome correlated with increased complement activation and with clinical variables reflecting the severity of acute hantavirus infection

The eBioKit, a stand-alone educational platform for bioinformatics

<div><p>Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.</p></div

An example of a lesson in the eBioKit training portal.

<p>The image displays an extract of the “Getting started” lesson for the tutorial “next-generation sequencing (NGS) analysis with Galaxy.” During a tutorial, the students will find multiple exercises that allow them to put into practice the content learned.</p

Web interface for the eBioKit.

<p>(A) The arrangement of the components that compose the web interface. Users can easily switch between the installed services on the eBioKit using the lateral menu. When users choose an option on the menu, the working area is replaced by the corresponding service and the menu is hidden, allowing users to fully interact with the service. (B), (C), and (D) show the familiar web interface users see when working with Ensembl Mammals, Galaxy, and MRS, respectively, in eBioKit. With the upper toolbar, users can open the services on a secondary window and, more importantly, can get a description as well as download documentation and tutorials for the selected service (E).</p