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Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server

A. Sczyrba, S. Konermann, R. Giegerich
2008 Briefings in Bioinformatics  
The Bielefeld Bioinformatics Server (BiBiServ) offers a variety of older and new materials.  ...  Here, we report on two online courses made available recently, one introductory and one on the advanced level: (i) SADR: Sequence Analysis with Distributed Resources  ...  This work was supported by grant BIZ 7 from the DFG-Initiative Bioinformatics.  ... 
doi:10.1093/bib/bbm063 pmid:18199576 fatcat:dxmlozvc2rbhrfgpk6wiw2lsz4

Bioinformatics core competencies for undergraduate life sciences education

Melissa A. Wilson Sayres, Charles Hauser, Michael Sierk, Srebrenka Robic, Anne G. Rosenwald, Todd M. Smith, Eric W. Triplett, Jason J. Williams, Elizabeth Dinsdale, William R. Morgan, James M. Burnette, Samuel S. Donovan (+23 others)
2018 PLoS ONE  
These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.  ...  Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students  ...  The authors also thank Sarah Moulton of Moulton Editorial Services (Omaha, Nebraska) for editing and formatting the final version of the manuscript.  ... 
doi:10.1371/journal.pone.0196878 pmid:29870542 pmcid:PMC5988330 fatcat:niuaiwdqwffpfoevfgh2trt4km

Benchmarking workflow discovery: a case study from bioinformatics

Antoon Goderis, Paul Fisher, Andrew Gibson, Franck Tanoh, Katy Wolstencroft, David De Roure, Carole Goble
2009 Concurrency and Computation  
To address their perceived lack of effective workflow discovery tools, we go on to develop benchmarks for the evaluation of discovery tools, drawing on a series of practical exercises.  ...  Based on a survey with participants from 19 laboratories, we investigate current practices in workflow sharing, re-use and discovery amongst life scientists chiefly using the Taverna workflow management  ...  Acknowledgment The authors are grateful to the Taverna training days participants, the myGrid team, the myExperiment team and Luna Dong for the Woogle source code. We also thank the  ... 
doi:10.1002/cpe.1447 fatcat:ck6dott5g5dnvjl5rttrhevy7y

Experiential Learning in Bioinformatics – Learner Support for Complex Workflow Modelling and Analysis

Vijini Mallawaarachchi, Anuradha Wickaramarachchi, Anuradha Weliwita, Indika Perera, Dulani Meedeniya
2018 International Journal of Emerging Technologies in Learning (iJET)  
One of the challenging areas for a student learning in bioinformatics is complex workflow modelling and analysis; it incorporates several threshold concepts and liminal spaces for student learning, which  ...  Better learning engagement during the experiment, better performance at advanced questions and a positive user response were observed from the students who used BioWorkflow tool, compared to the control  ...  The questions Q2 to Q6 are based on the theoretical knowledge the students have learnt whereas questions Q7 to Q10 examined the advanced skills that a student can apply their knowledge into a practical  ... 
doi:10.3991/ijet.v13i12.8608 fatcat:vtlq4fjfizet3bim7jl7zntrsq

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck
2013 BMC Bioinformatics  
To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal  ...  For bioinformatics, there is little practical information available regarding how to carry out UCD in practice.  ...  After selecting a number of data items users had to democratically vote to keep only six using the dot voting method [as described in [29] ). This was the prioritisation task of the exercise.  ... 
doi:10.1186/1471-2105-14-103 pmid:23514033 pmcid:PMC3623738 fatcat:lq4k3fmy45fsdmf5c7vjhxdt6u

Bioinformatics Core Competencies for Undergraduate Life Sciences Education [article]

Melissa A. Wilson Sayres, Charles Hauser, Michael Sierk, Srebrenka Robic, Anne G. Rosenwald, Todd M. Smith, Eric W. Triplett, Jason J. Williams, Elizabeth Dinsdale, William Morgan, James M. Burnette, Sam S. Donovan (+21 others)
2017 bioRxiv   pre-print
These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.  ...  Finally, we used the survey results, the analysis of syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate life sciences students  ...  Acknowledgements This material is based upon work supported by the National Science Foundation under Grant Number 1539900 to A.G.R., E.W.T., E.D., W.M., and M.A.P.  ... 
doi:10.1101/170993 fatcat:rp35gxmb7jbfbc5uoboquzduhu

A Bioinformatics Practicum to Develop Student Understanding of Immunological Rejection of Protein Drugs

Lauren A O'Donnell, Wilson S Meng, Benjamin J Andrick, Alexa M Borello
2016 American Journal of Pharmaceutical Education  
To design and implement a bioinformatics exercise that applies immunological principles to predicting rejection of protein drugs based upon patient genotype. Design.  ...  This study indicates that questions related to clinical immunology can be posed using bioinformatics tools.  ...  As science curriculum standards move toward problem-based and inquiry-based laboratory design, this exercise provides an opportunity to ask questions about the interactions of an important class of drugs  ... 
doi:10.5688/ajpe809147 pmid:28090096 pmcid:PMC5221830 fatcat:u6vysclxafcyxizllbcpnkmvqe

Dive in!

Michael Glueck, Azam Khan, Daniel J. Wigdor
2014 Proceedings of the 32nd annual ACM conference on Human factors in computing systems - CHI '14  
Figure 1: The Splash framework enables real-time navigation for client-server visualization systems by progressively loading data.  ...  Splash streamlines the process of creating a multiple level-of-detail version of the data and facilitates progressive data download, thereby enabling real-time, on-demand navigation with existing visualization  ...  ACKNOWLEDGEMENTS We would like to thank our reviewers, study participants, John Hancock, Katie Barker, John Stasko, and fellow DGP members for their insightful feedback.  ... 
doi:10.1145/2556288.2557195 dblp:conf/chi/GlueckKW14 fatcat:jacef3xfxrdgrpgn6fyngt72ai

11.1 Deliver The Identified Evaluation Systems And Good Practice Guidelines For Training. Deliver A Tess Platform And Identify E-Learning Solutions

Gabriella Rustici, Kim Gurwitz, Bellis Louisa, ELIXIR Training Community
2018 Zenodo  
It describes the achievements within the Task 11.1 of the WP11, Building the ELIXIR infrastructure. The deliverable in fact touches upon 3 subtasks (11.1.1, 11.1.2 and 11.1.3).  ...  This document (D11.1 - Deliver the identified evaluation systems and good practice guidelines for training.  ...  Each module includes a series of questions or 'Reflections' to provoke critical thinking about the tasks trainees have completed.  ... 
doi:10.5281/zenodo.1453020 fatcat:cqcpoyz26ngcdh646mc2nwewyi

Developing an online programme in computational biology

H. M. Vincent, C. Page
2012 Briefings in Bioinformatics  
Although this flexible approach fits the needs of course participants, it does not fit easily within the organizational structures of a campus-based university.  ...  Much has been written about the need for continuing education and training to enable life scientists and computer scientists to manage and exploit the different types of biological data now becoming available  ...  For example, our course in microarray data analysis is based around a series of exercises using Bioconductor [11] .  ... 
doi:10.1093/bib/bbs059 pmid:22988255 fatcat:c6ntzyl4afb2fahz4gsvptjp7i

Usability and Suitability of the Omics-Integrating Analysis Platform tranSMART for Translational Research and Education

C. Knell, A. Bosserhoff, E. Naschberger, M. Stürzl, M. Rübner, H. Seuss, M. Ruh, H.-U. Prokosch, B. Sedlmayr, J. Christoph
2017 Applied Clinical Informatics  
The test comprised 13 tasks in the context of four typical research scenarios based on experimental and clinical data.  ...  A web questionnaire was provided to identify both the needs and the conditions of research as well as to evaluate the system's usability based on the "System Usability Scale" (SUS).  ...  Acknowledgments The researchers who participated in this study are gratefully acknowledged for their precious time and effort. We also thank S. Newe and A.  ... 
doi:10.4338/aci-2017-05-ra-0085 pmid:29270954 pmcid:PMC5802312 fatcat:amrlgu6r6ff4nivevttuj7onma

Transparent access to multiple bioinformatics information sources

C. A. Goble, R. Stevens, G. Ng, S. Bechhofer, N. W. Paton, P. G. Baker, M. Peim, A. Brass
2001 IBM Systems Journal  
motif1)I \protein3 <-get-sp-entries-by-de("lard"), \protein2 <-do-blastp-by-sq-in-entry(protein3), Check-sp-entries-by-kwd("apoptosis",protein2), check-sp-entries-by-de("antigen",protein2), Check-sp-entry-for-species  ...  We are grateful for his contribution. **Trademark or registered trademark of Sun Microsystems, Inc., or Object Management Group.  ...  Acknowledgments This work is supported by the BBSRC/EPSRC Bioinformatics Programme grant BIF/05344, by AstraZeneca Pharmaceuticals, and by EPSRC grant GR/M76607 under the DIM initiative.  ... 
doi:10.1147/sj.402.0532 fatcat:5xnmkl2fvber3hyo3kmbn27pka

A Survey of Transfer and Multitask Learning in Bioinformatics

Qian Xu, Qiang Yang
2011 Journal of Computing Science and Engineering  
In this article, we survey recent advances in transfer and multitask learning for bioinformatics applications.  ...  Machine learning and data mining have found many applications in biological domains, where we look to build predictive models based on labeled training data.  ...  These works included regularization based methods, common feature representation based methods, distribution matching methods and their variants.  ... 
doi:10.5626/jcse.2011.5.3.257 fatcat:oruxwutza5godismndbqad2lm4

From command-line bioinformatics to bioGUI

Markus Joppich, Ralf Zimmer
2019 PeerJ  
Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines.  ...  Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary  ...  Jimenez-Soto and Gergely Csaba for their valuable input as well as for reviewing the manuscript. We thank the participants in our survey for their time.  ... 
doi:10.7717/peerj.8111 pmid:31772845 pmcid:PMC6875409 fatcat:lwvurr4fvzdvvf5xcdfzpy7xqi

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Nicola Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, Anne Rosenwald, Gabriella Rustici, Michael Sierk, Tandy Warnow, Lonnie Welch (+1 others)
2018 PLoS Computational Biology  
The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics  ...  Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare.  ...  As a proof of principle for ELIXIR, Europe's distributed infrastructure for biological data with nodes in 20 countries, EMBL-EBI and UCAM recently performed an exercise to map their course programmes to  ... 
doi:10.1371/journal.pcbi.1005772 pmid:29390004 pmcid:PMC5794068 fatcat:reaf6wxitjfbhfofxk3ipw77s4
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