January 2020 Galactic News

Events, Pubs, Blogs, Platforms, Tutorials, Doc, and Happy New Year too

January 8th 2020

Galaxy News

The January 2020 Galactic News is out:

If you have anything to include to next month's newsletter, then please send it to outreach@galaxyproject.org.

Events

There is an unusually rich (and aromatic!) mix of upcoming Galaxy related events:

Call for Tutorials
BCC2020: Call for Tutorial Nominations

The Bioinformatics Community Conference (BCC2020) needs

BCC is GCC + BOSC, and will be held in July in Toronto, right after ISMB 2020 in Montréal.

Galaxy Admin Training 2020
Register Now: Galaxy Admin Training 2020

Registration is now open for the 2020 Galaxy Admin Training being offered 2-6 March at the Barcelona Supercomputing Center. This week-long hands-on training will feature what you need to know to set up your own production quality Galaxy server. Space is limited.

Galaxy @ PAG 2020
Galaxy @ PAG 2020

Galaxy will be at Plant and Animal Genome XXVII (PAG 2020), in San Diego, California, United States, January 11-15. This includes a hands-on Galaxy Workshop (highlighting the new Excellence in Breeding platform) and many talks and posters featuring Galaxy.

And there will be a GMOD Codefest before PAG and an NCBI Codeathon after PAG.

Galaxy @ ABRF 2020
Galaxy @ ABRF 2020

Galaxy will be at 2020 ABRF meeting, in Palm Springs, California, United States, February 29 through March 3. This includes a full day hands-on Galaxy Workshop about using Galaxy with your single cell and microbiome data. ABRF is the annual conference for technology-enabled multidisciplinary research.

Early registration ends January 15. Space is limited.

Single-Cell RNAseq training at Earlham Institute
Single-Cell RNAseq training at Earlham Institute

An introduction to Single-Cell Genomics featuring Galaxy. This course is for bench-based researchers planning a single-cell project. Registration deadline is 2 March.

Traitement de données de séquences par Galaxy
Traitement de données de séquences par Galaxy

Introduction à la manipulation de données de régions génomiques et à l’analyse de jeux de données de type NGS via Galaxy.

Upcoming Events
Upcoming Events

There are

  • 13 upcoming events
  • on 3 continents, plus online
  • in US, Japan, Belgium, Germany, Spain, France, UK, and Canada.

Publications

172 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month. There were 9 Galactic and Stellar publications added, and 7 of them are open access. Some highlights:

Zanardi, N., Morini, M., Tangaro, M. A., Zambelli, F., Bosco, M. C., Varesio, L., … Cangelosi, D. (2019). Scientific Reports, 9(1), 1–12. doi: 10.1038/s41598-019-53155-9

Föll, M. C., Moritz, L., Wollmann, T., Stillger, M. N., Vockert, N., Werner, M., … Schilling, O. (2019). GigaScience, 8(12). doi: 10.1093/gigascience/giz143

Emami Khoonsari, P., Moreno, P., Bergmann, S., Burman, J., Capuccini, M., Carone, M., … Spjuth, O. (2019). Bioinformatics, 35(19), 3752–3760. doi: 10.1093/bioinformatics/btz160

Payá-Milans, M., Poza-Viejo, L., Martín-Uriz, P. S., Lara-Astiaso, D., Wilkinson, M. D., & Crevillén, P. (2019). GigaScience, 8(12). doi: 10.1093/gigascience/giz147

Etherington, G. J., Soranzo, N., Mohammed, S., Haerty, W., Davey, R. P., & Palma, F. D. (2019). A GigaScience, 8(12). doi: 10.1093/gigascience/giz144

Blum, M., Cholley, P.-E., Malysheva, V., Nicaise, S., Moehlin, J., Gronemeyer, H., & Mendoza-Parra, M. A. (2020). Life Science Alliance, 3(1). doi: 10.26508/lsa.201900546

Galactic Blog Activity

By Yvan Le Bras, Simon Bénateau.

Galaxy for Ecology, mixing Ecology research, Citizen Science and Massively Multi Online Science.

Crowdsourcing citizen science data on usegalaxy.eu

Galaxy Platforms News

The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. There are many new platforms this month:

Figure 1: PIPE-T Process

The GASLINI server supports PIPE-T, a tool for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis. Requires an account, but anyone can create an account.

Shapiro Lab

The Shapiro Lab at NCI provides RNA structure and design tools, including RNA2D3D and StructureLab, on a Galaxy virtual machine image.

Epigenomics with Galaxy and Jupyter

This Galaxy docker instance contains tools and workflows aimed at the analysis of epigenomics data, both ChIP-Seq and RNA-Seq.

UseGalaxy.*

Doc, Hub, and Training Updates

Then the Galaxy Training Network wants your feedback. Please take a few minutes to let us know about your training experiences.

Help! We need it!

By Bérénice Batut, Fotis E. Psomopoulos, Toby Hodges.

We believe that every learner can achieve competency with R. Give it a try.

R Basics in Galaxy

Lucille Delisle has updated the ATAC-Seq data analysis tutorial to add macs2 callpeak as an alternative to Genrich and addressed issues with bowtie indexes.

Heatmap results

By Bérénice Batut.

Clustering single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using Scanpy (Wolf et al. 2018).

QC Metrics

By Wendi Bacon, EMBL-EBI.

This webinar video highlights Galaxy interface for single cell analysis. Specifically it highlights Scanpy (which would otherwise require Python programming skills) to analyse a Drop-seq dataset located in EMBL-EBI's Single Cell Expression Atlas.

Single cell webcast video

Other News

Including a report about usegalaxy.eu and this year's community conference in Freiburg.

GCC2019

Galaxy is a prominent part of the NCI ITCR Program that funds tools that support the analysis of –omics, imaging, and clinical data, as well as network biology and data standards.

NCI ITCR

Dr Chris Barnett has invested in the research cloud-computing platform ilifu to create a central resource where a like-minded research community can come together and share these tools and expertise, using the opensource platform Galaxy.

UCT eResearch