Template -
Website name, website home page link, (website most recent paper), < Species_name> < isolate/strain> < Assembly and Gene set versions> .
+Species name, isolate/strain, assembly and gene set versions, website name, website home page link (website most recent paper).
Worked example for VectorBase -
For example if you want to reference your usage of the Anopheles gambiae AgamP4.13 genome you would use:
+For example if you want to reference your usage of the Anopheles gambiae AgamP4.13 and Aedes aegypti LVP_AGWG AaegL5.3 genomes you would use:
VectorBase, www.vectorbase.org (Giraldo-Calderón et al 2015), Anopheles gambiae PEST, AgamP4.13.
+Anopheles gambiae PEST AgamP4.13 and Aedes aegypti LVP_AGWG AaegL5.3, VectorBase + www.vectorbase.org + (Giraldo-Calderón et al 2022).
uid: cite-genome-assembly projects: "" - type: citing @@ -128,7 +131,7 @@Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y Basenko, Wojciech Bażant, Robert Belnap, Ann S Blevins, Ulrike Böhme, John Brestelli, Brian P Brunk, Mark Caddick, Danielle Callan, Lahcen Campbell, Mikkel B Christensen, George K Christophides, Kathryn Crouch, Kristina Davis, Jeremy DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I Giraldo-Calderón, Omar S Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A Kelly, Jessica C Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S Roos, Samuel S C Rund, Stephanie Wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J Stoeckert, Jr, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A Wilkinson, Lin Xu, Jie Zheng. (2021). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research (gkab929). https://doi.org/10.1093/nar/gkab929
Basenko, E. Y., Pulman, J. A., Shanmugasundram, A., Harb, O. S., Crouch, K., Starns, D., Warrenfeltz, S., Aurrecoechea, C., Stoeckert, C. J., Jr, Kissinger, J. C., Roos, D. S., & Hertz-Fowler, C. (2018). FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. Journal of fungi (Basel, Switzerland), 4(1), 39. https://doi.org/10.3390/jof4010039
Fischer, S., Brunk, B. P., Chen, F., Gao, X., Harb, O. S., Iodice, J. B., Shanmugam, D., Roos, D. S., & Stoeckert, C. J., Jr (2011). Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Current protocols in bioinformatics, Chapter 6, Unit–6.12.19. https://doi.org/10.1002/0471250953.bi0612s35
-Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., Ho, N., Gesing, S., VectorBase Consortium, Madey, G., Collins, F. H., & Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. https://doi.org/10.1093/nar/gku1117
+Giraldo-Calderón, G. I., Harb, O. S., Kelly, S. A., Rund, S. S., Roos, D. S., & McDowell, M. A. (2021). VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. Current opinion in insect science, 50, 100860. Advance online publication. https://doi.org/10.1016/j.cois.2021.11.008
Oliveira, F. S., Brestelli, J., Cade, S., Zheng, J., Iodice, J., Fischer, S., Aurrecoechea, C., Kissinger, J. C., Brunk, B. P., Stoeckert, C. J., Jr, Fernandes, G. R., Roos, D. S., & Beiting, D. P. (2018). MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic acids research, 46(D1), D684–D691. https://doi.org/10.1093/nar/gkx1027
Ruhamyankaka, E., Brunk, B. P., Dorsey, G., Harb, O. S., Helb, D. A., Judkins, J., Kissinger, J. C., Lindsay, B., Roos, D. S., San, E. J., Stoeckert, C. J., Zheng, J., & Tomko, S. S. (2020). ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates open research, 3, 1661. https://doi.org/10.12688/gatesopenres.13087.2
Older publications can be found under VEuPathDB Publications and Citations.
@@ -248,4 +251,4 @@mget gff/data/*
to get all files in that folder.
uid: programmaticallydownloadgenomefiles - projects: "" \ No newline at end of file + projects: "" diff --git a/_posts/.DS_Store b/_posts/.DS_Store index b50797868..4b491d8a1 100644 Binary files a/_posts/.DS_Store and b/_posts/.DS_Store differ diff --git a/_posts/news/ClinEpiDB/2022-03-03-clinepidb-21-released.html b/_posts/news/ClinEpiDB/2022-03-03-clinepidb-21-released.html new file mode 100644 index 000000000..08d55e5be --- /dev/null +++ b/_posts/news/ClinEpiDB/2022-03-03-clinepidb-21-released.html @@ -0,0 +1,36 @@ +--- +layout: post +title: ClinEpiDB 21 Released +category: [ClinEpiDB,AllClinEpiDB,release] +--- + + +Workshops and Webinars
+-
+
- ClinEpiDB is a resource where researchers can explore data shared by others and make their own de-identified data publicly accessible, and where students can access real-world data for use in epidemiology or biostatistics class projects and theses. If you have a departmental seminar or class where you would like us to give a presentation on what people can do with ClinEpiDB, please reach out to help@clinepidb.org! As part of our outreach efforts, we will be creating a 15-20 minute video aimed at students interested in accessing data via ClinEpiDB, which we can pair with live Q&A sessions for your class. +
New Features
+-
+
- The first six features listed below were previously debuted on beta.clinepidb.org. All eight features mentioned are now accessible on ClinEpiDB!
+
-
+
- A fresh new layout - An intuitive new layout lets you easily switch between viewing study info, browsing and subsetting data, and making plots and tables. And we save your place in each tab! At the top of the page, a diagram shows you the size and structure of the data. +
- Featured variables - Looking at a new study? The featured variables section highlights key variables for you to help you get started. +
- Starred variables - Star your favorite variables to access them more easily! This short list of variables can be used in the browse and subset tab and when making plots and tables in the visualize tab. +
- Browse and Subset tab - Create a subset of study data the way you're used to, by applying variable filters. As you create your subset, see the impact of filtering across the entire dataset by checking out the diagram at the top of the page! +
- Visualize tab - You can make histograms, bar plots, box plots, scatter plots, and mosaic plots for 2x2 and RxC contingency tables. You can also stratify by other variables, using overlays and facets. If you update your subset, no worries, your visualizations will automatically update when you reopen them. Check out this example where Weight-for-age-z-score is faceted by the Country of the study site. +
- Record Notes tab - If you open a study, there's a helpful new Record Notes tab where you can jot down your hypothesis, reminders about specific variables, plans to subset the data, interpretation of graphs, etc. Notes will be automatically saved as part of your analysis. +
- Download tab - From the Download tab, you can download either complete data files for a study, or configure download files that contain only the subset of data and variables you are interested in. +
- Share an analysis or make it public - If you subset the data within a study, create any visualizations, or add any notes, you can choose to share your analysis or make it publicly accessible. To share your analysis, click the "Share analysis" button, and you will generate a link that you can send to anyone. To make an analysis public, go to the "My analyses" page, find the analysis you want to make public, and click the checkbox. +
+
New Data
+-
+
- All 30 studies from our original site are accessible on the new ClinEpiDB platform via clinepidb.org. In addition, the Early Life Interventions for Childhood Growth and Development in Tanzania (ELICIT) study is the first study to be released only on the new platform! Expect to see the release of additional malaria studies, WASH studies, and maternal, newborn, and child health studies over the next few months! +
New data in FungiDB 56
Genome Sequence and Annotation: updated genomes
-
-
- Trichoderma reesei QM6a 2017 – +
- Trichoderma reesei QM6a – We are pleased to announce the first update for a FungiDB genome through Apollo, a web-based genomic annotation editing platform. We incorporated 225 changes, including creation of new genes, modification of existing genes, merges and splits. See a breakdown of the changes and the data incorporated.
Genome Sequence and Annotation:
+
Genome Sequence:
+-
+
+
- Raffaelea lauricola RL4 – + Zhang et al. 2020. + +
+
Whole genome sequence of isolates for SNP analysis:
- Aspergillus fumigatus diff --git a/_posts/news/ToxoDB/2022-02-15-toxodb-56-released.html b/_posts/news/ToxoDB/2022-02-15-toxodb-56-released.html index 00a87ad6e..3151007a4 100644 --- a/_posts/news/ToxoDB/2022-02-15-toxodb-56-released.html +++ b/_posts/news/ToxoDB/2022-02-15-toxodb-56-released.html @@ -22,7 +22,7 @@
- - RNA-seq of tartrolon E-treated T. gondii RH parasites – Transcriptome of Toxoplasma gondii parasites treated with 24.2 nM tartrolon E (trtE) or 0.1% DMSO control collected at 4, 8, and 12 h post-treatment. Data are aligned to T gondii ME49. Bowden et al. 2020. + RNA-seq of tartrolon E-treated T. gondii RH parasites – Transcriptome of Toxoplasma gondii parasites treated with 24.2 nM tartrolon E (trtE) or 0.1% DMSO control collected at 4, 8, and 12 h post-treatment. Data are aligned to T gondii ME49. Bowden et al. 2020.
New data in {{project}} 56
RNA Sequence
+We are pleased to announce a joint VEuPathDB and BV-BRC open community webinar series focusing on ticks and the bacterial, viral, or eukaryotic pathogens they transmit. Eight webinars will be held on a bi-weekly basis starting on March 8th. Each webinar will focus on specific data, tools, and functionality provided by these NIAID-funded bioinformatic resource centers. To learn more about these webinars and to register to attend please follow this link. + +
++
+ +
This video provides a quick start guide to our beta platform.
+This video provides a quick start guide to our new platform.
- Have an idea and don’t see it listed here? Please Contact Us. + Have an idea and don't see it listed here? Please Contact Us.
To stay up to date on ClinEpiDB releases, sign up for our newsletter by updating your account preferences. @@ -34,14 +34,12 @@ tags: [general]
- Perform boolean operations (find the intersection, union, or difference) for two data subsets
- Identify repeated measures that occurred within a specific time frame relative to another measure (e.g. all visits where a child had Shigella at least 7 days before having diarrhea) -
- Identify matched cases or controls for a case-control study
Visualizations
-
-
- Faceting - split one plot into multiple based on a categorical variable, with one plot for each type of value
- Marginal boxplots on histograms - enhance the view of the distribution
- Time series tool - plot data over time
- Map tool - view data geographically @@ -54,13 +52,6 @@ tags: [general]
Public analyses
-- Save your analyses and make them publicly accessible -
-DIY workspace
@@ -69,18 +60,18 @@ tags: [general]
Site Search
-Search ClinEpiDB and find studies containing variables of interest to you
-Cross-silo search
-Search for participants that have both epidemiological data in ClinEpiDB and microbiome data in our sister site MicrobiomeDB
--
-
- Introduction to ClinEpiDB and MicrobiomeDB +
- Introduction to ClinEpiDB and MicrobiomeDB
- Overview of workshop
-Structured exercise on navigating the ClinEpiDB beta platform +Structured exercise on navigating the ClinEpiDB beta platform
-Answer Key +Answer Key
Choice of:
- Formulating & reconfiguring simple searches: - Comparison of breastfeeding status and Giardia infection + Comparison of breastfeeding status and Giardia infection
- Discussion
-Getting started, creating a VEuPathDB account, and asking for help +Getting started, creating a VEuPathDB account, and asking for help
Review Search types, units of analysis, study designs -
Exercise: LLINEUP simple search +
Review Search types, units of analysis, study designs +
Exercise: LLINEUP simple search
Exercise: The Search Wizard- variable exploration -
Exercise: MAL-ED and GEMS1 simple search
Exercise: MAL-ED and GEMS1 simple search
Complex search with MAL-ED +
Complex search with MAL-ED
Visualization and analysis applications using SCORE data
Nupur Kittur
Exercise: Visualization and analysis apps -
Exercise: Complex searches using PROVIDE -
Exercise: PRISM analysis apps
Exercise: Visualization and analysis apps +
Exercise: Complex searches using PROVIDE +
Exercise: PRISM analysis apps
- Use Apollo to integrate new or update current structural and functional data, for gene models in the organisms available in VEuPathDB. + Use Apollo to integrate new or update current structural and functional data, for gene models in the organisms available in VEuPathDB.
We are currently in the process of a long term project to update our genome annotation which will mean some organisms are currently unavailable in Apollo. However, you can request these organisms to be available for curation by emailing our team at help@veupathdb.org for more information.
@@ -44,6 +44,7 @@ We are currently in the process of a long term project to update our genome anno- A "play" Apollo site, e.g., a sandbox (Login required) is available for you to experiment and get familiar with all Apollo menus, tools, and tracks before you decide to use it for your real gene manual annotations. These changes will not affect any of the organism's official gene set, neither will be preserved.
- A comprehensive webinar recording to learn how to use Apollo (57:40 min) +
- Check out our YouTube Apollo tutorial channel!
- A description of quick commands (Apollo now has the BLAT tool!)
- Functional annotation tutorial
- Structural annotation tutorial diff --git a/content/common/genomics_faq.md b/content/common/genomics_faq.md index f7ba567ea..e3fb2239b 100644 --- a/content/common/genomics_faq.md +++ b/content/common/genomics_faq.md @@ -25,7 +25,7 @@ div.static-content img { -
- Help improve genome annotations: provide evidence for alternative gene models, knockout phenotypes, sub-cellular localisation, PubMed IDs, etc. +
- Become immediately visible on the gene record pages & are searchable +
- Benefit the research community at large, showcase your favourite genes or publications, and are the quickest way to provide up-to-date information about genes on the live site +
- Sign in or Register at FungiDB.org +
- Navigate to the gene record page +
- Click on the Add a user comment link +
- Fill out the comment form (add text, pictures, files or PubMed IDs, etc.) +
- To submit user comments in bulk, download our bulk user comment submission form here: https://tinyurl.com/commentsfungi +
- Simply fill it out and send it back to us +
- Gene names, including synonyms, e.g. "Purine Phosphoribosyl Transferase, is also known as HPRT, HGPRT, Hypoxanthine Phosphoribosyltransferase, Ppt1, Ppt-1, etc.". Such information is critical if someone searching for HPRT. Include reference for each name if possible +
- PubMed IDs providing key reference materials for a gene (feel free to link any relevant papers, not just your own) +
- Functional characterization, e.g. "This hypothetical protein has been shown to be a copper transporter based on ... Contact [name] for further details" +
- Note that such information is most useful if associated evidence/contact is provided (can paste/upload text as an attachment) +
- Corrections (or even confirmation) of gene model predictions, annotations, etc. (with a brief description of the underlying evidence) +
- Image data … you can attach images to genes, providing subcellular localization, experimental evidence, etc.Subcellular localization, e.g. "GFP tagging demonstrates that this protein localizes to the mitochondrion, as shown in the attached images" +
- Phenotype data, e.g. you can provide phenotypic description for knockout and overexpression mutants +
- Structural information on annotated gene models, e.g. "The predominant transcript initiation site for this gene has been mapped to ~561 nt upstream of the annotated ATG by 5'RACE and RNAse protection. This conclusion is consistent with available RNAseq data, but differs from the reference annotation" Note that in addition to corrections to the reference annotation, experimental evidence supporting the reference annotation or offering insights into alternative transcripts is also very helpful +
- Other functional or experimental information (note that even negative data can be quite informative) +
- Analyzing data in Nephele - the National Institute of Allergy & Infectious Diseases microbiome analysis platform. @@ -247,7 +296,7 @@ bioinformatic resources available at FungiDB. Topic: The Bioinformatic Resource Centers Webinar Series: RSV, Pneumoviridae & ViPR
- abc -
- abc -
- abc -
- Site Search: use keywords (e.g., gene metadata and gene IDs), filter and explore results, export to strategies +
- Organism preferences: enable and disable to explore data sets +
- Gene pages: become familiar with the information on it, navigate to and from it, use the table of contents to navigate +
- Search strategies: how to construct and combine the more than 100 available searches to produce multi-step strategies, results can be in the format of gene IDs +
- RNAseq and microarrays data searches: use differential expression, fold change, and percentile searches to explore gene expression +
- Proteomics data searches: use mass spec data to identify genes based on expression evidence +
- Genome browser: use menu and navigation options, add and configure data tracks, interpret data (e.g. RNAseq) +
- Gene Ontology (GO) enrichment: run and analyze a GO enrichment analysis +
- Apollo: learn how to manually annotate a gene, which involves both structural changes (intron/exon boundaries) and metadata (gene name and symbol) +
- Galaxy: perform your own bioinformatic analysis using our servers, e.g. RNAseq transcript differential expression or SNP calling + -
- Number of course participants: maximum 30 -
- Registration will open on: 28 February 2022 -
- Registration may be made via this web form (this information is confidential and it helps us know our prospective audience to customize examples and exercises) -
- Registration deadline: while three is no deadline for registration, it will be taken on a first-come, first-served basis until we fill the workshop with 30 seats +
- Registration will open soon via the AGS website. After you complete your registration, you will receive an email from ggiraldo@nd.edu (Gloria I. Giraldo-Calderón) to fill out an online form, this process completes your registration. The form information is confidential and it helps us know our prospective audience to customize examples and exercises. +
- Registration deadline: it is the 29th of May 2022. It will be taken on a first-come, first-served basis
- Who should register: the ideal candidate should have a need to learn how to use VectorBase and be interested in using the database to answer their own research questions. Scientists at any career stage are welcome to apply -
- Number of course participants: maximum 30 -
- Registration will open on: 28 February 2022 -
- Registration may be made via this web form (this information is confidential and it helps us know our prospective audience to customize examples and exercises) -
- Registration deadline: while three is no deadline for registration, it will be taken on a first-come, first-served basis until we fill the workshop with 30 seats -
- Who should register: the ideal candidate should have a need to learn how to use VectorBase and presumably has a research question involving this database to help you solve it. Scientists at any career stage are welcome to apply. -
Home >> Help >> Learn how to use VEuPathDB >> FAQs - Explore
+Home >> Help >> Learn how to use VEuPathDB >> FAQs
Frequently Asked Questions
diff --git a/content/common/usercommentscampaign.md b/content/common/usercommentscampaign.md new file mode 100644 index 000000000..4ab6703bf --- /dev/null +++ b/content/common/usercommentscampaign.md @@ -0,0 +1,173 @@ +--- +layout: plain +title: VEuPathDB Workshops +permalink: /usercommentscampaign +tags: [workshop-exercise] +--- + + +
Home >> Help >> + Learn how to use VEuPathDB >> +
+ +FungiBD User Comments Campaign in conjunction with 31st Fungal Genetics Conference in Asilomar, USA
+Now and through March 19, 2022
+About the campaign
+Starting now and through the 31st Fungal Genetics Conference, add just one User Comment on a gene record page, and pick up your free "Got Fungus?" mug at the FungiDB help desk.
+Not attending in person? Not a problem! Ask a colleague to pick up your mug.
+ +Did you know that user comments:
+-
+
How to submit a single comment:
+-
+
How to submit user comments in bulk:
+-
+
Helpful User Comments Guide:
+As a rule of thumb, any information you wanted to know about a gene before you started working on it would be helpful ... but please do not duplicate automatically generated information, e.g. protein length, or the top BLAST hit.
+ +- Useful user comment examples:
-
+
Have questions? Contact Us
+ + diff --git a/content/common/webinars/tickWebinars.md b/content/common/webinars/tickWebinars.md index fed95e9c0..976c37354 100644 --- a/content/common/webinars/tickWebinars.md +++ b/content/common/webinars/tickWebinars.md @@ -94,13 +94,29 @@ th.recording { width: 20%; } + + +Home >> Help >> Learn how to use VEuPathDB >> + Webinars
+ + +Ticks and Tick-Borne Pathogens Open Community Webinar Series
Summary: This webinar series is geared towards researchers working on ticks and the bacterial, viral or eukaryoptic pathogens they transmit to humans. The webinars will focus on highlighting data and bioinformatic tools provided by the NIAID bioinformatic resource centers, VEuPathDB and BV-BRC. In addition, we welcome open discussion during the webinars so we can learn about your research needs the the BRCs might be able to provide.
-Structure: Demo of latest tools, data functionality. Open forum discussion. Opportunity to provide dataset suggestions, tool suggestions, data analysis issues.
+
+
+Summary: This webinar series is geared towards researchers working on ticks and the bacterial, viral or eukaryotic pathogens they transmit. The webinars will focus on highlighting data and bioinformatic tools provided by the NIAID bioinformatic resource centers, VEuPathDB and BV-BRC. In addition, we welcome open discussion during the webinars so we can learn about your research needs the the BRCs might be able to provide.
+
+Structure: Demo of latest tools, data functionality. Open forum discussion. Opportunity to provide dataset suggestions, tool suggestions, data analysis issues. Each session is scheduled for 1h.
+
Audience: The webinar series is free and open to all scientists from any career stage who may benefit from the BRCs.
+
+Participation: If you would like, please submit feedback or questions to be discussed during the webinars and, datasets suggestions to include in our databases, completing this webform. Alternatively, you can also participate live during the webinar.
+
+Recordings: We strongly value your participation and are looking forward to all your questions and feedback during our live sessions, but if you are unable to attend or would like to watch a session again, they will all be recorded and made available here.
+
All times in this schedule are given as Eastern Daylight time. Please @@ -113,65 +129,69 @@ th.recording {
+ Webinar slides +
+ Tutorial +
Home >> Help >> Learn how to use VEuPathDB >> Webinars - Explore
+Home >> Help >> Learn how to use VEuPathDB >> Webinars
VEuPathDB Webinars
@@ -25,7 +25,11 @@ tags: [general]Upcoming Webinars
Thursday February 24th, 2022: Release 56 Webinar
+Tuesday March 8 - June 14, 2022: Bi-weekly tick and tick pathogen webinar series
+Thursday April 28th, 2022: Release 57 Webinar
+Thursday July 7th, 2021: Release 58 Webinar
+Thursday September 29th, 2021: Release 59 Webinar
+Thursday November 10th, 2021: Release 60 Webinar
Previous Webinars
@@ -33,6 +37,7 @@ tags: [general] If you missed any of our previous webinars feel free to explore the free recordings: +Thursday February 24th, 2022: Release 56 Webinar
Thursday December 9th, 2021: Release 55 Webinar
Thursday September 16th, 2021: Release 54 Webinar
Thursday August 5th, 2021: Release 53 Webinar
@@ -85,24 +90,68 @@ tags: [general] Release webinar dates are subject to change due to production issues that may arise during a release. Registration links will be available 7-10 days prior to a release webinar.- +
-Date: Thursday Feb 24th, 2022
+Topic: Release 57 Webinar
+Date: Thursday April 28th, 2022
Time: 10AM US Eastern Time
-Registration: Available 7-10 days prior to webinar
-Additional Details: This webinar will focus on what is new in Release 56 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions. +Registraion: Registration links will be available 7-10 days prior to a release webinar.
+Additional Details: This webinar will focus on what is new in Release 57 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions. +
+
+ +
+Date: Thursday July 7th, 2022
+Time: 10AM US Eastern Time
+Registraion: Registration links will be available 7-10 days prior to a release webinar.
+Additional Details: This webinar will focus on what is new in Release 58 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions. +
+
+ +
+Date: Thursday September 25th, 2022
+Time: 10AM US Eastern Time
+Registraion: Registration links will be available 7-10 days prior to a release webinar.
+Additional Details: This webinar will focus on what is new in Release 59 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions. +
+
+ +
+Date: Thursday November 10th, 2022
+Time: 10AM US Eastern Time
+Registraion: Registration links will be available 7-10 days prior to a release webinar.
+Additional Details: This webinar will focus on what is new in Release 60 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions.
Previous Webinars
+ +
+Date: Thursday Feb 24th, 2022
+Time: 10AM US Eastern Time
+Recording: https://youtu.be/PANxoBp3Wf0
+Additional Details: This webinar will focus on what is new in Release 56 of the VEuPathDB projects. We will discuss new data sets, demonstrate searches and features, and answer questions. +
+
Date: Tuesday June 1st 2021
Time: 11AM US Eastern Time
-Recording Link: coming soon!
+Recording Link: https://youtu.be/GKNR3dViCcw
Additional Details: This webinar will focus on respiratory pathogens and introduce users to bioinformatic resources available at the Pathosystems Resource Integration Center.
@@ -207,7 +256,7 @@ bioinformatic resources available at the Pathosystems Resource Integration Cente Topic: The Bioinformatic Resource Centers Webinar Series: Enterovirus, Picornaviridae & ViPR
Date: Tuesday May 18th 2021
Time: 11AM US Eastern Time
-Recording Link: coming soon!
+Recording Link: https://youtu.be/G6MaVi5G2qY
Additional Details: This webinar will focus on respiratory pathogens and introduce users to bioinformatic resources available at the Virus Pathogen Resource.
@@ -219,7 +268,7 @@ bioinformatic resources available at the Virus Pathogen Resource. Topic: Web-based analysis of 16S rRNA microbiome data using Nephele and MicrobiomeDB
Date: Thursday May 6th, 2021
Time: 10AM US Eastern Time
-Recording Link: coming soon!
+Recording Link: https://vimeo.com/showcase/5598563/video/546055765
Additional Details: This webinar will focus on using web resources to analyze 16s rRNA microbiome, specifically:
Date: Tuesday April 20th, 2021
Time: 11AM US Eastern Time
-Registration: https://jcvi.webex.com/jcvi/j.php?RGID=r3305a49424c66191b85bc2d62611dc74
+Recording Link: https://youtu.be/Wv0xUZKLDHg
Additional Details: This webinar will focus on respiratory pathogens and introduce users to bioinformatic resources available at the Virus Pathogen Resource.
@@ -289,6 +338,7 @@ bioinformatic resources available at the Virus Pathogen Resource. Topic: The Bioinformatic Resource Centers Webinar Series: AMR, bacteria & PATRIC
Date: Tuesday March 30th, 2021
Time: 11AM US Eastern Time
+Recording: https://youtu.be/SaKKUIIwDG0
Additional Details: This webinar focused on respiratory pathogens and introduced users to bioinformatic resources available at the Pathosystems Resource Integration Center.
Date: Tuesday March 16th, 2021
Time: 11AM US Eastern Time
-Recording Link:
+Recording Link: https://youtu.be/zB_wKXqn54U
Additional Details: This webinar will focus on respiratory pathogens and introduce users to bioinformatic resources available at the Virus Pathogen Resource.
Date: Tuesday February 16th, 2021
Time: 11AM US Eastern Time
-Recording:
+Recording:https://youtu.be/VP7d1XYIWdM
Additional Details: This webinar focused on respiratory pathogens and introduced users to bioinformatic resources available at the Influenza Research Database.
Home >> Help >> Learn how to use VEuPathDB >> Workshops - Explore
+Home >> Help >> + Learn how to use VEuPathDB >> + Workshops
VEuPathDB Workshops
Arthropod Genomicis Symposium 2022: pre-meeting VectorBase hands-on Workshop
- Sunday June 5th 2022, at 6pm (Sunday) to Thursday June 9th, 2022 at 12pm (noon) -Room location to be confirmed (in Person, University of Notre Dame, Notre Dame, IN)
+6:00 pm on Sunday, 5th June to 12:00 pm (noon) on Thursday, 9th June 2022
+Jordan Hall of Science, University of Notre Dame, Notre Dame, IN
+In-person (sessions will not be virtual or recorded)
About the workshop
-This is a 5-day intensive workshop that will provide you with hands-on training on how to effectively use VectorBase to mine the available data and to analyze your own data. Since VectorBase is part of the VEuPathDB Bioinformatics Resource Center, all learned knowledge can be applied to its other components such as those supporting vector-transmitted pathogens Plasmodium (PlasmoDB), Leishmania, Trypanosoma (TriTrypDB), Babesia, and Theileria (PiroplasmaDB). -
+This is a 5-day intensive workshop that will provide you with hands-on training on how to effectively use VectorBase to mine the available data and to analyze your own data. Since VectorBase is part of the VEuPathDB Bioinformatics Resource Center (BRC), all learned knowledge can be applied to its other components such as those supporting vector-transmitted pathogens Plasmodium (PlasmoDB), Leishmania, Trypanosoma (TriTrypDB), Babesia, and Theileria (PiroplasmaDB).
-Expected learning objectives:
+Expected learning objectives:
-
-
This workshop is scheduled as a symposium pre-event, and even if you are not attending AGS, you are more than welcome to attend the workshop. -
- -COVID-19
-As As this is an in-person event (sessions will not be virtual or recorded), we will comply with all the host campus COVID-19 policies and guidelines as presented here: covid.nd.edu.
+This workshop is scheduled as a symposium pre-event, and even if you are not attending AGS, you are more than welcome to attend the workshop.
+COVID-19 safety
+We encourage all workshop attendees to wear face coverings while indoors, regardless of vaccination status. Please see the AGS website for more information.
About us
-If you are a new user and will like to know more details about our resources to decide if you want to apply for the workshop, we invite you to read our more recent VEuPathDB (Aurrecoechea et al 2022) and VectorBase (Giraldo-Calderón et al 2022) papers, and explore our free tutorials and previously recorded webinars and workshops (https://vectorbase.org/vectorbase/app/static-content/landing.html). If you attend or not the workshop, please feel free to email us (help@vectorbase.org), our goal is to maintain a fruitful and ongoing conversation between our team and you, the scientists working in medical entomology, to obtain more efficient, effective ways to help you reach your goals.
+If you are a new user and will like to know more details about our resources to decide if you want to apply for the workshop, we invite you to read our more recent VEuPathDB (Amos et al 2022) and VectorBase (Giraldo-Calderón et al 2022) papers, and explore our free tutorials and previously recorded webinars and workshops. Regardless of if you attend or not the workshop, please feel free to email us (help@vectorbase.org), our goal is to maintain a fruitful and ongoing conversation between our team and you, the scientists working in medical entomology, to obtain more efficient, effective ways to help you reach your goals.
Computer and internet access
-A A room with computers will not be provided, please bring your own laptop. It should have the latest Firefox, Google Chrome, Safari or Microsoft edge versions installed. +
A room with computers will not be provided, please bring your own laptop. It should have the latest Firefox, Google Chrome, Safari or Microsoft edge version installed.
Registration
Cost and fees
-The registration fee is $ 60 USD, payments should be made using this AGS-University of Notre Dame link. The registration fee includes learning materials and some meals (see agenda for details).
-You are expected to provide your own transportation, lodging, and additional meals. At your request, we can email you a registration acceptance letter to facilitate your application for external travel funds or scholarships.
+The registration fee is $ 65 USD, payments should be made using this AGS-University of Notre Dame link. The registration fee includes learning materials and some meals (see agenda for details). You are expected to provide your own transportation, lodging, and additional meals. At your request, we can email you a registration acceptance letter to facilitate your application for external travel funds or scholarships. AGS is offering a travel award, follow this link for details, we strongly encourage to you apply for it.
Lodging
-If you prefer to stay on campus for the workshop, University of Notre Dame Morris Inn (https://morrisinn.nd.edu/) and the XYZ dorm (which dorm has been reserved?) single room accommodations are available for you at the special rate of XYZ with the promo code xyz. There are only a few rooms available for the workshop participants and we do expect these to fill up quickly.
+We have rooms reserved at the University of Notre dame dorms and hotel, please see the AGS website for more information.
Weather
Buildings in the summer might be very cold, you might want to plan to bring a sweater. The month with the most rain in Indiana is June, it is a good idea to have an umbrella.
Questions
-Please direct inquiries or questions to help@vectorbase.org
+Please direct inquiries or questions to help@vectorbase.org
Instructors
@@ -181,27 +186,32 @@ div.centered-title {Philadelphia, PA, USA
Members of the VEuPathDB outreach team
++
-
David S. Roos
-
Joint-PI, NIAID BRC Contract; WT Co-PI
+
+
David S. Roos, PhD
+
Joint-PI, VEuPathDB NIAID-NIH Contract; WT Co-PI
University of Pennsylvania
Philadelphia, PA, USA
Guest instructors
-Mary Ann McDowell, PhD
-
Joint-PI, VectorBase/VEuPathDB NIAID-NIH Contract
+
Joint-PI, VectorBase NIAID-NIH Contract
University of Notre Dame
Notre Dame, IN, USA
+
+
Robert Waterhouse, PhD
University of Lausanne
The Swiss Institute of Bioinformatics
Switzerland
+
- -
Schedule
| 6:00 - 9:00 pm | -Registration and welcome dinner + | Registration + Welcome dinner (provided) General introduction to omics Attendees introductions Group photo |
GIGC, OH, MAM, DSR, SR |
+
+
+ +
| DSR |
||||
| 12:00 pm | +12:00 m | Lunch (provided) | ||
| 2:30 pm | Coffee/Tea Break (provided) | -- |
+ ||
| 2:50 pm | Homology gene relationships via OrthoMCL DB | -GIGC - |
+ GIGC |
|
| 4:00 pm - 5:00 pm | -RNA sequence data analysis via Galaxy, Part I starting the workflow (Group Exercise) | -OSH - |
+ RNA sequence data analysis via Galaxy, Part II starting the workflow (Group Exercise) | +OSH |
+
+ +
| Time | Topic (and handout) | -Instructor | - +Instructor | |||
|---|---|---|---|---|---|---|
| 8:00 am | Breakfast (provided) | - - |
-
+ |
|||
| 9:00 AM | +9:00 am | Sequence Exercises: Motifs, domains and colocation | GIGC | -|||
| 9:30 AM | +9:30 am | Data retrieval and download | -GICG - |
-
+ GICG |
||
| 10:00 am | Coffee/Tea Break (provided) | - | ||||
| 10:50 AM | -Identifying SNPs using Galaxy, Part I (Group exercise) | -OSH - |
- + | 10:50 am | +RNA sequence data analysis via Galaxy, Part III: DESeq2 and Exporting your data to VectorBase
+ FASTQ Groomer + Trimmomatic + FASTQC + HISAT2 + bamCoverage + htseq-count + HTSeqCountToTPM |
+ OSH |
| 12:00 PM | +12:00 pm | Lunch (provided) | -- |
-
+ |||
| 1:00 PM | -Gene models discussion and day wrap up | -David Roos - |
-
+ 1:00 pm | +RNA sequence data analysis via Galaxy, Part IV: viewing and analyzing your results, Bam to BigWig (Group Exercise) | +OSH |
|
| 1:00 PM | -Free option discussion and questions | -- |
- - |
+ 2:30 pm | +Coffee/Tea Break (provided) | +|
| 1:30 PM | -Zoom closes | -- |
- - |
+ 2:50 pm | +Functional Genomics 1: Transcriptomics, Proteomics, GO Enrichment, Metabolic Pathways | +GIGC |
| 4:00 - 5:00 pm | +Workshop group project, Part 1: Define your own questions and develop a method to answer them with VectorBase (Group exercise) | +
+
+
+
| Time | -Event and PDF handouts | +Topic (and handout) | Instructor | -|||
|---|---|---|---|---|---|---|
| 8:30am | -Zoom session opens | -- |
- - |
+ 8:00 am | +Breakfast (provided) | +|
| 9:00 AM | -Introduction to Galaxy in VEuPathDB | -Omar Harb | - +9:00 am | +Population data with MapVEu: population abundance, pathogen infection status, insecticide resistance genotypes and phenotypes, blood meal host, microsatellites and SNP data … etc. | +SR | |
| 10:00 AM | -Transcriptomic and Proteomics data | -Susanne Warrenfeltz | - +10:00 am | +Coffee/Tea Break (provided) | +||
| 10:30 AM | - -Break out | -- |
+ 10:20 am | +Population data with the genome browser: SNPs | +SR |
|
| 11:00 AM | -Break | -- |
-
+ 11:00 am | +RNA sequence data analysis Part V: finish data analyses | +OSH |
|
| 11:30 AM | -Exercise: Transcriptomics and proteomics (Cont.) | -Break out | -- |
+ 12:00 m | +Lunch (provided) | +|
| 12:00 PM | -Introduction to Orthology | -Mark Hickman | - +1:00 pm | +Functional Genomics 2: Host response data | +GIGC | |
| 12:45 PM | -Wrap up and Discussion | -Evelina Basenko + | 2:00 pm | +Workshop group project, Part 2: Data analyses (Group exercise)
+ Start outline of presentation, you can do a live demo and/or a few slides |
-
+ ||
| 1:00 PM | -Free option discussion and questions | -- |
- - |
+ 3:00 pm | +Coffee/Tea Break (provided) | +|
| 1:30 PM | -Zoom closes | -- |
- - |
+ 3:20 - 5:00 pm | +Workshop group project, Part 3: Finalize project (Group exercise) | +
+
+ +
| Time | -Event and PDF handouts | +Topic (and handout) | Instructor | -|||
|---|---|---|---|---|---|---|
| 8:30am | -Zoom session opens | - - |
- - |
- |||
| 9:00 AM | -Galaxy in VEuPathDB - understanding output files and what to do - with them. | -- Mark Hickman, Kathryn Crouch and Omar Harb - |
- Lecture - |
- |||
| 9:30 AM | -Ontologies and Enrichment analysis | -Mark Hickman - |
- Lecture - |
- |||
| 9:45 AM | -abc | -Break out - |
- - |
- |||
| 11:00 AM | -Break | -- |
- - |
- |||
| 11:30 AM | -Phenotypic data | -Evelina Basenko | -Lecture - |
+ 8:00 am | +Breakfast (provided) | + |
| 12:00 PM | -abc | -Break out - |
- - |
+ 9:00 am | +Manual gene annotation with Apollo | +GIGC, RW |
| 12:45 PM | -Final wrap up | -All - |
- - |
+ 10:30 am | +Coffee/Tea Break (provided) | +|
| 1:00 PM | -Free option discussion and questions | -- |
- - |
+ 10:50 am | +Workshop group project, Part 4: Present your findings | +|
| 1:30 PM | -Zoom closes | -- |
- - |
+ 12:00 - 12:15 pm | +Workshop Feedback and wrap-up. Digital certificates will be provided. | +
Sponsored and organized by
- INSER LOGOS HERE - ++
+
Sponsored and organized by
+Home >> Help >> Learn how to use VEuPathDB >> Workshops - Explore
+Home >> Help >> Learn how to use VEuPathDB >> Workshops
VEuPathDB Workshops
Upcoming Workshops
- -Arthropod Genomicis Symposium 2022: pre-meeting VectorBase hands-on Workshop
- 6:00pm on Sunday, 5th June to 12:00pm (noon) on Thursday, 9th 2022 -(In Person, University of Notre Dame, Notre Dame, IN)
+Arthropod Genomicis Symposium 2022: pre-meeting VectorBase hands-on Workshop
+6:00pm on Sunday, 5th June to 12:00pm (noon) on Thursday, 9th June 2022
+Jordan Hall of Science, University of Notre Dame, Notre Dame, IN
+In-person (sessions will not be virtual or recorded)
@@ -155,531 +154,9 @@ th.recording {
- - - -
-
Upcoming Workshops - Details
-- -
Arthropod Genomicis Symposium 2022: pre-meeting VectorBase hands-on Workshop
-6:00pm on Sunday, 5th June to 12:00pm (noon) on Thursday, 9th 2022
-Room location to be confirmed (in Person, University of Notre Dame, Notre Dame, IN)
- -About the workshop
-Over 5 days, we will provide a thorough and intensive introduction to VectorBase +50 genomes, other data, tools, and resources, which are part of the VEuPathDB Bioinformatics Resource Center. All the demonstrations and exercises will be done with VectorBase, which is exactly the same page layout and tools as any of the other VEuPathDB resources, which include pathogens transmitted by vectors such as Plasmodium, Leishmania, Trypanosoma, Babesia, and Theileria.
-The workshop is centered on determining what is — and isn't — working for you, the end-user. Our goal is to maintain a fruitful and ongoing conversation between our team and you, the scientists working in medical entomology, to obtain more efficient, effective ways to help you reach your goals. We hope this experience is as beneficial for you as it is for us, and we look forward to learning together.
-This workshop is scheduled as a symposium pre-event, and even if you are not attending AGS, you are more than welcome to attend the workshop.
- -COVID-19
-As this is an in-person event (sessions will not be virtual or recorded), we will comply with all the host campus COVID-19 policies and guidelines as presented here: covid.nd.edu.
- -About us
-If you are a new user and will like to know more details about our resources to decide if you want to apply for the workshop, we invite you to read our more recent VEuPathDB (Aurrecoechea et al 2022) and VectorBase (Giraldo-Calderón et al 2022) papers, and explore our free tutorials and previously recorded webinars and workshops (https://vectorbase.org/vectorbase/app/static-content/landing.html).
- -Computer and internet access
-A room with computers will not be provided, please bring your own laptop. It should have the latest Firefox, Google Chrome, Safari or Microsoft edge versions installed.
- -Registration
--
-
Cost and fees
-The registration fee is $ 60 USD, payments should be made using this AGS-University of Notre Dame link. The registration fee includes learning materials and some meals (see agenda for details).
-You are expected to provide your own transportation, lodging, and additional meals. At your request, we can email to you a registration acceptance letter to facilitate your application for external travel funds or scholarships.
- -Lodging
-If you prefer to stay on campus for the workshop, University of Notre Dame Morris Inn (https://morrisinn.nd.edu/) and the XYZ dorm (which dorm has been reserved?) single room accommodations are available for you at the special rate of XYZ with the promo code xyz. There are only a few rooms available for the workshop participants and we do expect these to fill up quickly.
- -Weather
-Buildings in the summer might be very cold, you might want to plan to bring a sweater. The month with the most rain in Indiana is June, it is a good idea to have an umbrella.
- -Questions
-Please direct inquiries or questions to help@vectorbase.org
- -Instructors
- --
Gloria I. Giraldo-Calderón, PhD
-Samuel Rund, PhD
-University of Notre Dame
-Notre Dame, IN, USA
-- -
-
Omar Harb, PhD
-University of Pennsylvania
-Philadelphia, PA, USA
-- -
-
Members of the VEuPathDB outreach team
-- -
Guest instructors
- --
Mary Ann McDowell, PhD
-Joint-PI, VectorBase/VEuPathDB NIAID-NIH Contract
-University of Notre Dame
-Notre Dame, IN, USA
--
-
Christopher Childers, PhD
-Monica Poelchau, PhD
-USDA-ARS, National Agricultural Library
-Beltsville, MD, USA
-- -
-
Robert Waterhouse, PhD
-University of Lausanne
-The Swiss Institute of Bioinformatics
-Switzerland
-- - -
Schedule
- -| Sunday, 5th June 2022 | -|||
|---|---|---|---|
| Time | -Topic (and handout) | -Instructor | -DELETE | -
| 6:00 - 9:00 pm | -Registration and welcome dinner - General introduction to omics - Attendees introductions - Group photo - | -GIGC, OH, SR, MAM | -- |
-
| 8:00 am | -Breakfast (provided) | -- | - - |
-
| 9:00 am | -VectorBase general introduction: remit, data tools and resource | -GIGC | - - |
-
| 9:30 am | -Search: Finding genes (with Site Search and BLAST), building search strategies and visiting gene pages | -GIGC - |
- - |
-
| 10:00 am | -Coffee/Tea Break (provided) | -- |
- - |
-
| 10:20 am | -Search -- Continued | -GIG - |
- - |
-
| 11:00 am | -Genome Browser I: Alignments and Comparative Genomics | -- |
- - - |
-
| 12:00 pm | -Lunch (provided) | -- |
- - |
-
| 1:00 pm | -RNA sequence data analysis via Galaxy, Part I Uploading data (Group Exercise) | -- |
- - |
-
| 1:45 pm | -Genome Browser II: Interpreting RNAseq data | -- |
- - |
-
| 2:30 pm | -Coffee/Tea Break (provided) | -- |
- - |
-
| 2:50 pm | -Homology gene relationships via OrthoMCL DB | -GIGC - |
- - |
-
| 4:00 pm - 5:00 pm | -RNA sequence data analysis via Galaxy, Part I starting the workflow (Group Exercise) | -- |
- - |
-
-
| Tuesday, 7th June 2022 | -|||
|---|---|---|---|
| Time | -Topic (and handout) | -Instructor | -DELETE | -
| 8:00 am | -Breakfast (provided) | - - |
- - |
-
| 9:00 AM | -Sequence Exercises: Motifs, domains and colocation | -GIGC | -- |
-
| 9:30 AM | -Data retrieval and download | -GICG - |
- - |
-
| 10:00 am | -Coffee/Tea Break (provided) | -- | - |
-
| 11:00 AM | -Break | -- |
- - |
-
| 11:30 AM | -Exploring Gene models in the genome browser | -Break out - |
- - |
-
| 12:30 PM | -Gene models discussion and day wrap up | -David Roos - |
- - |
-
| 1:00 PM | -Free option discussion and questions | -- |
- - |
-
| 1:30 PM | -Zoom closes | -- |
- - |
-
-
| Wednesday, December 15th | -|||
|---|---|---|---|
| Time | -Event and PDF handouts | -Instructor | -Recording | -
| 8:30am | -Zoom session opens | -- |
- - |
-
| 9:00 AM | -Introduction to Galaxy in VEuPathDB | -Omar Harb | -- |
-
| 10:00 AM | -Transcriptomic and Proteomics data | -Susanne Warrenfeltz | -- |
-
| 10:30 AM | -Transcriptomic exercise -Proteomics exercise |
- Break out | -- |
-
| 11:00 AM | -Break | -- |
- - |
-
| 11:30 AM | -Exercise: Transcriptomics and proteomics (Cont.) | -Break out | -- |
-
| 12:00 PM | -Introduction to Orthology | -Mark Hickman | -- |
-
| 12:45 PM | -Wrap up and Discussion | -Evelina Basenko - |
- - |
-
| 1:00 PM | -Free option discussion and questions | -- |
- - |
-
| 1:30 PM | -Zoom closes | -- |
- - |
-
-
| Thursday, December 16th | -|||
|---|---|---|---|
| Time | -Event and PDF handouts | -Instructor | -Recording | -
| 8:30am | -Zoom session opens | - - |
- - |
-
| 9:00 AM | -Galaxy in VEuPathDB - understanding output files and what to do - with them. | -- Mark Hickman, Kathryn Crouch and Omar Harb - |
- Lecture - |
-
| 9:30 AM | -Ontologies and Enrichment analysis | -Mark Hickman - |
- Lecture - |
-
| 9:45 AM | -GO Enrichment | -Break out - |
- - |
-
| 11:00 AM | -Break | -- |
- - |
-
| 11:30 AM | -Phenotypic data | -Evelina Basenko | -Lecture - |
-
| 12:00 PM | -Phenotypic Data | -Break out - |
- - |
-
| 12:45 PM | -Final wrap up | -All - |
- - |
-
| 1:00 PM | -Free option discussion and questions | -- |
- - |
-
| 1:30 PM | -Zoom closes | -- |
- - |
-
Sponsored and organized by
- INSER LOGOS HERE +Previous Workshops - Details
@@ -694,7 +171,7 @@ th.recording {9AM - 1PM US Eastern time
Registration deadline: December 6, 2021
-Annual VEuPathDB Workshop 2021 (Virtual)
@@ -1188,7 +668,7 @@ th.recording {Datasets and Instructions
Datasets and Instructions
-
VectorBase: Previous tutorials - and Previous workshops and webinars.
-VEuPathDB: Previous workshops.
-