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Establishment of “The South African Bioinformatics Student Council” and Activity Highlights “南非生物信息学学生会”成立及活动亮点
EMBnet.journal Pub Date : 2018-02-02 DOI: 10.14806/EJ.23.0.903
Candice Rafael, J. Ambler, Antoinette Niehaus, James Ross, Ö. T. Bishop
{"title":"Establishment of “The South African Bioinformatics Student Council” and Activity Highlights","authors":"Candice Rafael, J. Ambler, Antoinette Niehaus, James Ross, Ö. T. Bishop","doi":"10.14806/EJ.23.0.903","DOIUrl":"https://doi.org/10.14806/EJ.23.0.903","url":null,"abstract":"The South African Bioinformatics Student Council (SASBiSC) in bioinformatics has been set up to increase the visibility of bioinformatics as well as to filter information to students within the field regarding job, funding and workshop opportunities as they arise. This is a short description of the process of setting up a national Student Council for Bioinformatics in South Africa, affiliating to the International Society for Computational Biology (ISCB). We also report two examples of activities that were carried out over the last two years that are: 1) participation in the SciFest Africa; and 2) the organisation of the first Bioinformatics Student Symposium.  We hope that our experience and methods for the creation of SASBiSC and of collaborative communities can be useful to others who might want to do the same.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"14 1","pages":"903"},"PeriodicalIF":0.0,"publicationDate":"2018-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88267662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Mobile microscopy for the examination of blood samples 用于检查血液样本的移动显微镜
EMBnet.journal Pub Date : 2018-02-02 DOI: 10.14806/EJ.23.0.904
J. Pfeil, M. Frohme, Katja Schulze
{"title":"Mobile microscopy for the examination of blood samples","authors":"J. Pfeil, M. Frohme, Katja Schulze","doi":"10.14806/EJ.23.0.904","DOIUrl":"https://doi.org/10.14806/EJ.23.0.904","url":null,"abstract":"The analysis of blood is one of the best possibilities to diagnose and control diseases and deficiency symptoms. Common blood tests that are performed in medical laboratories are time-consuming and work-intensive. In under-developed areas, there is often also a lack of specialised staff and facilities. The development of a mobile microscopic system that contains an automated image analysis and that can be used via a smartphone, could represent a valuable help to improve the diagnostic care, especially in those areas. it aims to enable a very fast, cheap, location- and knowledge-independent application for many use cases.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"95 1","pages":"904"},"PeriodicalIF":0.0,"publicationDate":"2018-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89980108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Report on the “Big Data Training School for Life Sciences”, 18-22 September 2017, Uppsala, Sweden “生命科学大数据培训学校”报告，2017年9月18日至22日，瑞典乌普萨拉
EMBnet.journal Pub Date : 2018-02-02 DOI: 10.14806/EJ.23.0.905
J. Pfeil, Sabrina K. Schulze, Eftim Zdravevski, Yen Hoang
{"title":"Report on the “Big Data Training School for Life Sciences”, 18-22 September 2017, Uppsala, Sweden","authors":"J. Pfeil, Sabrina K. Schulze, Eftim Zdravevski, Yen Hoang","doi":"10.14806/EJ.23.0.905","DOIUrl":"https://doi.org/10.14806/EJ.23.0.905","url":null,"abstract":"In September 2017 a \"Big Data Training School for Life Sciences\" took place in Uppsala, Sweden, jointly organised by EMBnet and the COST Action CHARME (Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research - CA15100). The week programme was divided into hands-on sessions and lectures. In both cases, insights into dealing with big amounts of data were given. This paper describes our personal experience as students’ by providing also some suggestions that we hope can help the organisers as well as other trainers to further increase the efficiency of such intensive courses for students with diverse backgrounds.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"19 1","pages":"905"},"PeriodicalIF":0.0,"publicationDate":"2018-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82389831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Genomic big data hitting the storage bottleneck. 基因组大数据遭遇存储瓶颈。
EMBnet.journal Pub Date : 2018-01-01 Epub Date: 2018-04-19
Louis Papageorgiou, Picasi Eleni, Sofia Raftopoulou, Meropi Mantaiou, Vasileios Megalooikonomou, Dimitrios Vlachakis
{"title":"Genomic big data hitting the storage bottleneck.","authors":"Louis Papageorgiou,&nbsp;Picasi Eleni,&nbsp;Sofia Raftopoulou,&nbsp;Meropi Mantaiou,&nbsp;Vasileios Megalooikonomou,&nbsp;Dimitrios Vlachakis","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>During the last decades, there is a vast data explosion in bioinformatics. Big data centres are trying to face this data crisis, reaching high storage capacity levels. Although several scientific giants examine how to handle the enormous pile of information in their cupboards, the problem remains unsolved. On a daily basis, there is a massive quantity of permanent loss of extensive information due to infrastructure and storage space problems. The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data. To bring sequencing to the foreground, scientists have to slide over such obstacles and find alternative ways to approach the issue of data volume. Scientific community experiences the data crisis era, where, out of the box solutions may ease the typical research workflow, until technological development meets the needs of Bioinformatics.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"24 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40437933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Spotlight 197 蛋白质聚焦197
EMBnet.journal Pub Date : 2017-12-15 DOI: 10.14806/ej.23.0.909
EMBnet journal
{"title":"Protein Spotlight 197","authors":"EMBnet journal","doi":"10.14806/ej.23.0.909","DOIUrl":"https://doi.org/10.14806/ej.23.0.909","url":null,"abstract":"","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"14 1","pages":"909"},"PeriodicalIF":0.0,"publicationDate":"2017-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73403079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Spotlight 195 蛋白质聚焦195
EMBnet.journal Pub Date : 2017-12-15 DOI: 10.14806/ej.23.0.907
EMBnet journal
{"title":"Protein Spotlight 195","authors":"EMBnet journal","doi":"10.14806/ej.23.0.907","DOIUrl":"https://doi.org/10.14806/ej.23.0.907","url":null,"abstract":"","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"51 1","pages":"907"},"PeriodicalIF":0.0,"publicationDate":"2017-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90864937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Spotlight 191 蛋白质聚焦191
EMBnet.journal Pub Date : 2017-12-15 DOI: 10.14806/ej.23.0.906
EMBnet journal
{"title":"Protein Spotlight 191","authors":"EMBnet journal","doi":"10.14806/ej.23.0.906","DOIUrl":"https://doi.org/10.14806/ej.23.0.906","url":null,"abstract":"","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"42 1","pages":"906"},"PeriodicalIF":0.0,"publicationDate":"2017-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80840445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Spotlight 196 蛋白质聚焦196
EMBnet.journal Pub Date : 2017-12-15 DOI: 10.14806/EJ.23.0.908
EMBnet journal
{"title":"Protein Spotlight 196","authors":"EMBnet journal","doi":"10.14806/EJ.23.0.908","DOIUrl":"https://doi.org/10.14806/EJ.23.0.908","url":null,"abstract":"","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"1 1","pages":"908"},"PeriodicalIF":0.0,"publicationDate":"2017-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88670632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Galaksio, a user friendly workflow-centric front end for Galaxy Galaksio，一个用户友好的工作流程为中心的前端Galaxy
EMBnet.journal Pub Date : 2017-11-16 DOI: 10.14806/EJ.23.0.897
T. Klingström, R. Hernández-de-Diego, Théo Collard, E. Bongcam-Rudloff
{"title":"Galaksio, a user friendly workflow-centric front end for Galaxy","authors":"T. Klingström, R. Hernández-de-Diego, Théo Collard, E. Bongcam-Rudloff","doi":"10.14806/EJ.23.0.897","DOIUrl":"https://doi.org/10.14806/EJ.23.0.897","url":null,"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 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 functions as a stand-alone server that can be configured for to be connected to any Galaxy server using the Galaxy API. Galaksio can be downloaded at: https://github.com/fikipollo/galaksio .","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"10 1","pages":"897"},"PeriodicalIF":0.0,"publicationDate":"2017-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80426089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
InSyBio ncRNASeq: A web tool for analyzing non-coding RNAs InSyBio ncRNASeq:一个分析非编码rna的web工具
EMBnet.journal Pub Date : 2017-10-12 DOI: 10.14806/EJ.23.0.882
A. Korfiati, K. Theofilatos, Christos Alexakos, S. Mavroudi
{"title":"InSyBio ncRNASeq: A web tool for analyzing non-coding RNAs","authors":"A. Korfiati, K. Theofilatos, Christos Alexakos, S. Mavroudi","doi":"10.14806/EJ.23.0.882","DOIUrl":"https://doi.org/10.14806/EJ.23.0.882","url":null,"abstract":"Non-coding RNA (ncRNA) genes are RNA molecules transcribed from DNA, but not translated to proteins. Instead, they are involved in gene regulatory mechanisms and a variety of other cellular processes, and they have been associated with several diseases. Thus, their accurate and efficient identification as well as the identification of the genes they regulate is a promising research area and an open topic for the bioinformatics community. In the present paper, we present InSyBio ncRNASeq, which is a cloud-based web platform assisting users to analyze ncRNA sequences and predict whether they are miRNAs, pseudo-hairpins or if they belong to another ncRNA category. Additionally, InSyBio ncRNASeq offers a unique miRNA target prediction pipeline, which results in scored miRNA target sites in genes’ 3’UTRs. This tool not only presents the highest accuracy metrics compared with other state of the art methods and tools, but also offers batch searches between many or all known human miRNAs and many mRNAs.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"29 1","pages":"882"},"PeriodicalIF":0.0,"publicationDate":"2017-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84577062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
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