| 1. |
- Hernandez De Diego, Rafael, et al.
(författare)
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The eBioKit, a stand-alone educational platform for bioinformatics
- 2017
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Ingår i: {PLOS} Computational Biology. - : Public Library of Science (PLoS). - 1553-7358. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
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| 3. |
- Klingström, Tomas
(författare)
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Biobanking in Emerging Countries
- 2013
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Ingår i: Biopreservation and Biobanking. - : Mary Ann Liebert Inc. - 1947-5535 .- 1947-5543. ; 11, s. 329-330
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Annan publikation (refereegranskat)
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| 4. |
- Klingström, Tomas, et al.
(författare)
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Biobanking in emerging countries, a special issue on challenges and opportunities
- 2013
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Ingår i: ESBB Conference. ; , s. 1 p-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Swedish University of Agricultural Sciences, Uppsala, Sweden. Biobanking in emerging countries faces different and more challenging requirements than biobanking in nations with more developed infrastructure. The description of methods developed under these challenging conditions may not only be valuable to scientists facing similar obstacles, but may also be valuable to other researchers as these innovative methods, when developed, may prove more reliable and cost effective than the more established methods. The journal of Biopreservation and Biobanking and the Molecular Methods database are therefore collaborating in the creation of a special issue on biobanking in emerging countries to be published in October 2013. This presentation will provide an overview over key topics covered in the issue and also provide some informal lessons learned from working with the issue. Biopreservation and Biobanking is the first journal to provide a unifying forum for peer-reviewed communication of recent advances in the rapidly emerging field of biospecimen procurement, processing, preservation, and banking. The Molecular methods database (www.molmeth.org) is a completely free and open access website supported by BBMRI.se and the Affinomics project to store and publish laboratory protocols as well as other "how to" information in biological science.
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| 5. |
- Klingström, Tomas, et al.
(författare)
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Evaluation of machine learning algorithms on protein-protein interactions
- 2014
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Ingår i: Man-Machine Interactions 3. Advances in Intelligent Systems and Computing. - Cham : Springer International Publishing. - 9783319023083 ; 242:242, s. 211-218
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Protein-protein interactions are important for the majority of biological processes. A significant number of computational methods have been developed to predict protein-protein interactions using proteins' sequence, structural and genomic data. Hence, this fact motivated us to perform a comparative study of various machine learning methods, training them on the set of known protein-protein interactions, using proteins' global and local attributes. The results of the classifiers were evaluated through cross-validation and several performance measures were computed. It was noticed from the results that support vector machine outperformed other classifiers. This fact has also been established through statistical test, called Wilcoxon rank sum test, at 5% significance level.
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| 6. |
- Klingström, Tomas, et al.
(författare)
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Galaksio, a user friendly workflow-centric front end for Galaxy
- 2017
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Ingår i: EMBnet.journal. - : EMBnet Stichting. - 2226-6089. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- There is a severe shortage of statisticians and bioinformaticians available in research. As universities fail to cover the increasing need of graduates with the necessary skills, ad hoc training and workshops have become commonplace but are insufficient to cover the needs. Technical solutions that distribute the workload more efficiently between researchers with a different education background (e.g., computer scientists and biologists) are therefore necessary to cover some of this shortage. Galaksio provides a workflow-centric graphical user interface for the Galaxy Workflow Management system that is easy to use for biologists and medical researchers who need to run routine tasks in bioinformatics. Combined with back end tools such as BioBlend, CloudMan and Pulsar, Galaksio provides a novel, layered approach to Galaxy making it easier to divide research tasks to researchers depending on their skills in interdisciplinary subjects such as bioinformatics and computational science. Galaksio is developed by the B3Africa project for the eB3Kit but can easily be installed independently using docker and configured to provide access to workflows on any Galaxy server using the Galaxy API. Galaksio can be downloaded at: https://github.com/fikipollo/galaksio.
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| 7. |
- Klingström, Tomas, et al.
(författare)
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Legal & ethical compliance when sharing biospecimen
- 2018
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Ingår i: Briefings in Functional Genomics & Proteomics. - Oxford : Oxford University Press. - 2041-2649 .- 2041-2657. ; 17:1, s. 1-7
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 10. |
- Klingström, Tomas, et al.
(författare)
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Protein-protein interaction and pathway databases, a graphical review
- 2011
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 12:6, s. 702-713
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Forskningsöversikt (refereegranskat)abstract
- The amount of information regarding protein-protein interactions (PPI) at a proteomic scale is constantly increasing. This is paralleled with an increase of databases making information available. Consequently there are diverse ways of delivering information about not only PPIs but also regarding the databases themselves. This creates a time consuming obstacle for many researchers working in the field. Our survey provides a valuable tool for researchers to reduce the time necessary to gain a broad overview of PPI-databases and is supported by a graphical representation of data exchange. The graphical representation is made available in cooperation with the team maintaining www.pathguide.org and can be accessed at http://www.pathguide.org/interactions.php in a new Cytoscape web implementation. The local copy of Cytoscape cys file can be downloaded from http://bio.icm.edu.pl/similar to darman/ppi web page.
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