EMBnet.journal最新文献_第10页

PolarFCS: A Multi-Parametric Data Visualisation Aid for Flow Cytometry Assessment PolarFCS:用于流式细胞术评估的多参数数据可视化辅助工具

EMBnet.journal Pub Date : 2017-10-10 DOI: 10.14806/EJ.23.0.892

Pavandeep Gill, J. Luider, E. Mahé

{"title":"PolarFCS: A Multi-Parametric Data Visualisation Aid for Flow Cytometry Assessment","authors":"Pavandeep Gill, J. Luider, E. Mahé","doi":"10.14806/EJ.23.0.892","DOIUrl":"https://doi.org/10.14806/EJ.23.0.892","url":null,"abstract":"Currently available Flow-Cytometry Software (FCS) analysis platforms are computationally efficient and user-friendly, but may lack the functionality of single-plot, multi-parametric data visualisation. Methods to overcome this include gating techniques and/or dimensionality reduction. However, these strategies make Flow-Cytometry (FC) data analysis more time- and labour-intensive; profound errors can also result from incorrect FCS use. We have developed PolarFCS, a software tool capable of single-plot, multi-parametric data visualisation. Unlike traditional clinical FC plots, which typically operate directly on a data-set to produce single-parameter FC histograms or two-parameter orthogonal scatter plots, PolarFCS operates on the flow-parameter calculated centre of mass of each event in the data-set, and presents these as a dot-plot. We compare PolarFCS to our traditional clinical FCS workflow, using a selection of clinical plasma cell FC data. Multiple flow plots and gating strategies are required in the traditional software to isolate neoplastic populations. In PolarFCS, however, positional re-arrangement and scaling of the poles can be used to quickly isolate a population of interest. We also compare both approaches in a case of Minimal Residual Disease (MRD) assessment, and again, the versatility of the polar adjustment and parameter scaling allowable with PolarFCS is demonstrated. PolarFCS employs strategies that allow more accurate, standardised and detailed FC data analysis compared to traditional FCS platforms. Visualisation of multiple parameters in a single plot is an effective and invaluable feature that many other platforms currently do not offer. Availability: PolarFCS can be downloaded at https://github.com/etiennemahe/PolarFCS","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"58 1","pages":"892"},"PeriodicalIF":0.0,"publicationDate":"2017-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91368174","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

H3ABioNet: Developing Sustainable Bioinformatics Capacity in Africa H3ABioNet:发展非洲可持续的生物信息学能力

EMBnet.journal Pub Date : 2017-05-17 DOI: 10.14806/EJ.23.0.886

N. Mulder, S. Aron, Sumir Panji, Kim T. Gurwitz, Judit Kumuthini, S. Baichoo, S. Fatumo, O. Nash, Jonathan, Kayondo, Faisal M. Fadlelmola, S. Kassim, O. O. M. Oukem-Boyer, S. P. Salifu, Lerato E. Magosi, Victoria Nembaware, Mary Piper, Radhika S. Khetani, Anne Fischer

{"title":"H3ABioNet: Developing Sustainable Bioinformatics Capacity in Africa","authors":"N. Mulder, S. Aron, Sumir Panji, Kim T. Gurwitz, Judit Kumuthini, S. Baichoo, S. Fatumo, O. Nash, Jonathan, Kayondo, Faisal M. Fadlelmola, S. Kassim, O. O. M. Oukem-Boyer, S. P. Salifu, Lerato E. Magosi, Victoria Nembaware, Mary Piper, Radhika S. Khetani, Anne Fischer","doi":"10.14806/EJ.23.0.886","DOIUrl":"https://doi.org/10.14806/EJ.23.0.886","url":null,"abstract":"The diverse, rapidly developing discipline of bioinformatics has become an integral component of all areas of biomedical research in recent years. The ability to manage, analyse and interpret large complex datasets hinges on having access to skilled researchers who have received adequate training in specialised technical areas. Currently in Africa, individuals with these specialised skills are sparsely scattered across the continent and there is an urgent need to develop sustainable training programs to improve bioinformatics capacity. As part of the Human Heredity and Health in Africa (H3Africa) initiative, a pan-African bioinformatics network for H3Africa (H3ABioNet) was established to develop bioinformatics infrastructure together with a sustainable high quality training program. Here, we discuss the various training events and approaches developed by H3ABioNet to address the lack of bioinformatics capacity in Africa, together with the valuable lessons learnt.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"91 1","pages":"886"},"PeriodicalIF":0.0,"publicationDate":"2017-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82378749","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: 12

A stepping stone to develop bioinformatics in Pakistan 在巴基斯坦发展生物信息学的跳板

EMBnet.journal Pub Date : 2017-05-12 DOI: 10.14806/EJ.23.0.891

S. Manzoor, A. Niazi, E. Bongcam-Rudloff

引用次数: 3

A report on the “International Society for Computational Biology - Latin America (ISCB-LA)” Bioinformatics Conference 2016 2016年“国际计算生物学学会-拉丁美洲(ISCB-LA)”生物信息学会议报告

EMBnet.journal Pub Date : 2017-04-28 DOI: 10.14806/EJ.23.0.883

Nicolás Palopoli, A. M. Monzon, G. Parisi, A. Chernomoretz, Fernán Agüero

引用次数: 2

Bioinformatics activities at the University Hospital San Martino IST in Genoa 热那亚圣马蒂诺IST大学医院的生物信息学活动

EMBnet.journal Pub Date : 2017-04-28 DOI: 10.14806/EJ.23.0.884

P. Romano

引用次数: 0

2016 EMBnet Annual General Meeting – Executive Board Report 2016年EMBnet年度股东大会-执行董事会报告

EMBnet.journal Pub Date : 2017-04-18 DOI: 10.14806/EJ.22.0.887

D. D’Elia, E. B. Hernández, L. Klucar, E. Bongcam-Rudloff

引用次数: 0

ENJ Editorial Assistant Activity Report ENJ编辑助理活动报告

EMBnet.journal Pub Date : 2017-03-09 DOI: 10.14806/EJ.22.0.881

Antonio Santovito

引用次数: 0

Set up your own bioinformatics server: Chipster in EGI Federated Cloud 建立您自己的生物信息学服务器:EGI联邦云中的Chipster

EMBnet.journal Pub Date : 2017-02-06 DOI: 10.14806/EJ.22.0.879

K. Mattila, Diego Scardaci, M. Antonacci, C. Condurache

{"title":"Set up your own bioinformatics server: Chipster in EGI Federated Cloud","authors":"K. Mattila, Diego Scardaci, M. Antonacci, C. Condurache","doi":"10.14806/EJ.22.0.879","DOIUrl":"https://doi.org/10.14806/EJ.22.0.879","url":null,"abstract":"Chipster is an easy to use data analysis platform for bioinformatics. It provides an uniform graphical interface for over 360 commonly used bioinformatics tools including several R/Bioconductor-based tools and standalone programs (i.e. BWA, TopHat). Chipster is based on a client-server system where the user runs locally a Chipster-client that submits analysis tasks to a Chipster server. Even though Chipster is an open source tool, there is no public Chipster server that would be open for everybody. Due to that, a researcher needs to have an access to some of the existing Chipster servers to be able to use this platform. Alternatively, a researcher can set up his own Chipster server. In this paper, we describe how a Chipster server can be launched EGI Federated Could environment, that provides resources for all European researchers. With the instructions provided here, any European researcher can launch and manage his own Chipster server, suited for needs of a small research group or a bioinformatics course. The setup described here is based on a collaboration of several European instances. Chipster is developed by CSC – IT Center for Science Ltd. in Finland. European Grid Infrastructure (EGI) has fitted Chipster to cloud environment and provides the cloud computing resources. Finally, Rutherford Appleton Laboratory hosts the CVMFS server that provides the scientific tools and data sets for the Chipster servers running in EGI federated cloud.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"57 1","pages":"879"},"PeriodicalIF":0.0,"publicationDate":"2017-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91064726","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

InSyBio BioNets: an efficient tool for network-based biomarker discovery InSyBio bioonets:基于网络的生物标志物发现的有效工具

EMBnet.journal Pub Date : 2016-12-05 DOI: 10.14806/EJ.22.0.871

K. Theofilatos, Christos M. Dimitrakopoulos, Christos E. Alexakos, A. Korfiati, S. Likothanassis, S. Mavroudi

引用次数: 4

Protein Spotlight 183 蛋白质聚焦183

EMBnet.journal Pub Date : 2016-11-22 DOI: 10.14806/ej.22.0.875

EMBnet journal

引用次数: 0