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73 materials found

Target audience: Life Science Researchers 


Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis https://tess.elixir-europe.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Helis Academy - FAIRify your data https://tess.elixir-europe.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
Online course 'Learn to write your Data Management Plan'

Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for...

Keywords: Data management plan, data management

Resource type: e-learning

Online course 'Learn to write your Data Management Plan' https://tess.elixir-europe.org/materials/online-course-learn-to-write-your-data-management-plan Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for you research project. While you are training, you can write your DMP in DMPonline. You can do the whole course or just parts of it. That is all up to you. Data management plan, data management Life Science Researchers
Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course materials

Ready For BioData Management? https://tess.elixir-europe.org/materials/ready-for-biodata-management "Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences. Marta Silva Data management Data managment plan Life Science Researchers PhD students Master students Technicians
Research Data Management and Sharing

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Resource type: e-learning

Research Data Management and Sharing https://tess.elixir-europe.org/materials/research-data-management-and-sharing This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans, and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories. Today, an increasing number of funding agencies, journals, and other stakeholders are requiring data producers to share, archive, and plan for the management of their data. In order to respond to these requirements, researchers and information professionals will need the data management and curation knowledge and skills that support the long-term preservation, access, and reuse of data. Effectively managing data can also help optimize research outputs, increase the impact of research, and support open scientific inquiry. After completing this course, learners will be better equipped to manage data throughout the entire research data lifecycle from project planning to the end of the project when data ideally are shared and made available within a trustworthy repository. This course was developed by the Curating Research Assets and Data Using Lifecycle Education (CRADLE) Project in collaboration with EDINA at the University of Edinburgh. This course was made possible in part by the Institute of Museum and Library Services under award #RE-06-13-0052-13. The views, findings, conclusions or recommendations expressed in this Research Data Management and Sharing MOOC do not necessarily represent those of the Institute of Museum and Library Services. Data management Life Science Researchers
Research Data Management

Welcome to Research Data Management Training for Information Professionals! This course will provide you with training on the research data management (RDM) topics listed below in a biomedical context. The material presented began as an NIH-funded research study to assess material for teaching...

Scientific topics: Data management

Resource type: e-learning

Research Data Management https://tess.elixir-europe.org/materials/research-data-management Welcome to Research Data Management Training for Information Professionals! This course will provide you with training on the research data management (RDM) topics listed below in a biomedical context. The material presented began as an NIH-funded research study to assess material for teaching RDM to librarians. It is designed to prepare you to understand and subsequently teach RDM at your own institution, and offers strategies for identifying opportunities to teach RDM in your own environment. At the end of each module there is a link to a Teaching Toolkit that provides librarians with a script, slides, and evaluation materials to teach RDM at your institution. Data management Life Science Researchers
Tools for data management planning

Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you...

Scientific topics: Data management

Keywords: Data managment plan

Resource type: Video

Tools for data management planning https://tess.elixir-europe.org/materials/tools-for-data-management-planning Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you have never made a data management plan before the process may initially seem daunting, but fortunately there are many tools out there to help you think through the what, where, how, why and when of data management. In this webinar Sarah Jones from the Digital Curation Centre and Rob Hooft from ELIXIR Netherlands show us two tools - DMP online and the ELIXIR Data Stewardship Wizard - and explain how they can help you apply data management and FAIR data practices in your own research. Data management Data managment plan Life Science Researchers
What happens to your data?

This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data...

Scientific topics: Data management

Keywords: metadata, ArrayExpress

Resource type: Video

What happens to your data? https://tess.elixir-europe.org/materials/what-happens-to-your-data This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data and give examples of how metadata and standards are used when you submit data to Metabolights and ArrayExpress. They also answer a few frequently asked data submission-related questions. Data management metadata, ArrayExpress Life Science Researchers
Why share your data?

Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we...

Scientific topics: Data management

Keywords: data sharing

Resource type: Video

Why share your data? https://tess.elixir-europe.org/materials/why-share-your-data Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we approach biology and how EMBL-EBI provides some of the infrastructure to allow data sharing. He finishes up by highlighting the benefits of data sharing to the EMBL-EBI and shares his top four reasons for sharing data. Our second speaker, Elisabeth Busch, is the head of the Vertebrate Genetics and Genomics Group at the Wellcome Sanger Institute and the University of Cambridge. She tells us about her experiences in sharing her own research data, and the reasons that she felt compelled to share her data including the advantages for her own research. Elisabeth Busch Data management data sharing Life Science Researchers
A FAIRy tale

A FAKE STORY IN A TRUSTWORTHY GUIDE TO THE FAIR PRINCIPLES FOR RESEARCH DATA

Scientific topics: Data management

Keywords: FAIR

Resource type: PDF

A FAIRy tale https://tess.elixir-europe.org/materials/a-fairy-tale A FAKE STORY IN A TRUSTWORTHY GUIDE TO THE FAIR PRINCIPLES FOR RESEARCH DATA Data management FAIR Life Science Researchers
eLearning course about the importance of good research data management (RDM)

Within the framework of the Danish National Forum for Data Management, the Danish Universities have developed the eLearning course “Research Data Management”. This eLearning course in Research Data Management is brought to you by the Danish National Forum for Data Management, and is funded by...

Scientific topics: Data management

Resource type: Video

eLearning course about the importance of good research data management (RDM) https://tess.elixir-europe.org/materials/elearning-course-about-the-importance-of-good-research-data-management-rdm Within the framework of the Danish National Forum for Data Management, the Danish Universities have developed the eLearning course “Research Data Management”. This eLearning course in Research Data Management is brought to you by the Danish National Forum for Data Management, and is funded by Denmark’s Electronic Research Library (DEFF) and the Danish eInfrastructure Cooperation (DeiC). Data management Life Science Researchers
FAIRification & Data modelling

Wikidata fairification

Keywords: FAIR, linked data, ontologies, metadata

Resource type: Slides

FAIRification & Data modelling https://tess.elixir-europe.org/materials/fairification-data-modelling Wikidata fairification FAIR, linked data, ontologies, metadata Life Science Researchers bioinformaticians
Helis Academy - Persistent identifiers and their use cases

Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source

Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

Resource type: Slides

Helis Academy - Persistent identifiers and their use cases https://tess.elixir-europe.org/materials/persistent-identifiers-and-their-use-cases Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source Referencing data and code, Findability of data and code, Identifying data and code, data management data stewards Life Science Researchers bioinformaticians
Introduction to FAIR data stewardship

FAIR data Stewardship: How to improve the reuse of nanosafety data

Scientific topics: Data management

Keywords: FAIR

Introduction to FAIR data stewardship https://tess.elixir-europe.org/materials/introduction-to-fair-data-stewardship FAIR data Stewardship: How to improve the reuse of nanosafety data Data management FAIR Life Science Researchers
Helis Academy - Data Management Plans, why and how?

Research Data Management The organisation of data throughout the research project everyday management of research data (storage, file naming, preservation) how will data be preserved and shared after the project is completed?

Scientific topics: Data management

Keywords: Data managment plan, Data Life Cycle

Resource type: Slides, PDF

Helis Academy - Data Management Plans, why and how? https://tess.elixir-europe.org/materials/data-management-plans-why-and-how Research Data Management The organisation of data throughout the research project everyday management of research data (storage, file naming, preservation) how will data be preserved and shared after the project is completed? Data management Data managment plan, Data Life Cycle Life Science Researchers
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Computer science, Bioinformatics, Biology

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Computer science Bioinformatics Biology High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics https://tess.elixir-europe.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R https://tess.elixir-europe.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers
InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine user manual

Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine.

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine user manual https://tess.elixir-europe.org/materials/intermine-user-manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians
Probabilistic programming with (R)Stan

Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be...

Scientific topics: Statistics and probability

Probabilistic programming with (R)Stan https://tess.elixir-europe.org/materials/probabilistic-programming-with-r-stan Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be implemented, improved, and critizised in a flexible, explicit and transparent manner, and the analysis can be supported with prior information about the data. This 1-day course provides an introduction to Bayesian/probabilistic models. We will implement standard linear models based on the rstanarm package of the R statistical programming environment and readily available example data sets. The workshop is an ideal opportunity to familiarize yourself with the basic ideas in probabilistic modeling such as prior information, likelihood, model criticism and validation, as well as some of the available tools. At the end, you should be able to implement basic probabilistic models yourself, and understand their relative advantages and pitfalls compared to their classical alternatives. Statistics and probability Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
Image Ethics and Poster Design

The image ethics part handles on the theoretical aspects of image manipulation, the mistakes people make and how to avoid image fraud. VIB has guidelines for acceptable scientific image manipulations. Not all manipulations are scientifically correct. There are manipulations that fall within the...

Scientific topics: Image

Image Ethics and Poster Design https://tess.elixir-europe.org/materials/image-ethics-and-poster-design The image ethics part handles on the theoretical aspects of image manipulation, the mistakes people make and how to avoid image fraud. VIB has guidelines for acceptable scientific image manipulations. Not all manipulations are scientifically correct. There are manipulations that fall within the scope of scientific misconduct, because they result in misrepresentation of the data. Such misrepresentation makes it impossible for others to interpret the data correctly, or worse, leads to conclusions that are not correct. The second part of this course deals with poster design. Scientific posters are a resume of a piece or timespan of research on one square meter of paper. They are best compared to slides for oral presentations, not a written document. Posters can’t convey detailed evidence like scientific articles, it must visualize a message on its own. When standing a meter away from a poster you hardly feel like reading much text, especially when the author/designer stands next to it. A poster must bring that message without requiring oral explanation, but with as little text as possible. Prerequisites Participants must have experience with GIMP and Inkscape. Schedule See the TRAINING AT VIB website for a detailed schedule of this training. Training material Not available Links Not available Scientific topics Image data Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians   Image Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
Analysis of metabolome data

This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of...

Scientific topics: Metabolomics

Analysis of metabolome data https://tess.elixir-europe.org/materials/analysis-of-metabolome-data This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of differential metabolites will be introduced. Afterwards, the trainee should be able to perform independently a comparative analysis of raw metabolome data and to pinpoint the well-known metabolites in the chromatogram. Metabolomics Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
Advanced FlowJo training

The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high...

Advanced FlowJo training https://tess.elixir-europe.org/materials/advanced-flowjo-training The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high dimensionality. Prerequisites Participants must have experience with FlowJo. Schedule See the TRAINING AT VIB website for a detailed schedule of this training. Training material Not available Links Not available Scientific topics FlowJo Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
A tour of machine learning - classification

Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses,...

Scientific topics: Machine learning

A tour of machine learning - classification https://tess.elixir-europe.org/materials/a-tour-of-machine-learning-classification Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses, gene/protein annotation, drug design, image recognition, text mining and many others. However, building successful machine learning models requires a substantial amount of “black art” that is hard to find in textbooks. This course is an interactive Jupyter Notebook (Python) that will teach you how to build successful machine learning models. No background in machine learning is assumed, just a keen interest. Machine learning Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
Introduction to Biopython

Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient. The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the...

Scientific topics: Software engineering

Introduction to Biopython https://tess.elixir-europe.org/materials/introduction-to-biopython-8ccf2441-bd7d-46f2-84f8-c2b123844a23 Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient. The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the command line. Afterwards you will take a tour of the most important components: sequences, NCBI queries, BLAST, trees, and 3D structures. You will try each of these modules on practical examples. Please don't hesitate to ask questions about Python basics or particular data formats (e.g. XML or NGS data). The second day of the training is to broaden your perspective: What other features does the library have? How can you use the documentation effectively? What is Biopython not capable of? What can I do to visualize my data? Are there alternatives? If you have your own data that you would like to work on with Biopython in more detail, there is room for that. For us, the most important thing is to identify concrete Python modules and functions that help you to get your research done. Participants are encouraged to submit a description of their research topic and/or the questions they would like to answer with Biopython. Additionally, participants can bring their own data that they would like to process in Python to the training. Software engineering Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
Electronic Lab Notebook Introduction - Ghent

The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates,...

Electronic Lab Notebook Introduction - Ghent https://tess.elixir-europe.org/materials/electronic-lab-notebook-introduction The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Metagenomics

This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the...

Metagenomics https://tess.elixir-europe.org/materials/metagenomics This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the training will give an overview of numerical ecology and takes part entierly in R. post-docs PhD students beginner bioinformaticians Life Science Researchers 2016-04-22 2016-08-31
RNA-Seq analysis for differential expression in GenePattern

We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to...

RNA-Seq analysis for differential expression in GenePattern https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression-in-genepattern We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to compensate for artefacts like duplicates Calculate transcript counts usable for differential expression and merging of count tables Computing differential expression using EdgeR and DESeq2 The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training. Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
Custom training: Ingenuity Pathway Analysis

The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes,...

Scientific topics: Microarray experiment, Proteomics, Protein interactions, Metabolomics

Custom training: Ingenuity Pathway Analysis https://tess.elixir-europe.org/materials/custom-training-ingenuity-pathway-analysis The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes, networks and pathways mapping a list of genes/proteins/chemicals mapping quantitative data e.g. microarray/proteomics/metabolomics data High quality visualisation of biological networks and pathways Assessing the biological significance of pathways in certain physiological conditions e.g. detecting overrepresented pathways in diseases Microarray experiment Proteomics Protein interactions Metabolomics Life Science Researchers post-docs PhD students 2016-04-22 2016-09-26