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<details open> <summary>

Nanotate Annotations Samples

</summary> ```json [ { "id":"d5JrdABbEeuatj9X3vvoXw", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:50:41.265044+00:00", "updated":"2020-09-27T00:50:41.265044+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"", "prefix":"for 10 minutes. Wash with PBS3. ", "exact":"Add imaging buffer with desired ratios of Buffer C (500 mM), ethylene carbonate, and IS-CF660R at 1-2 nM final concentration. The exact concentration of IS may need to be adjusted depending on the target and based on the imaging kinetics.", "suffix":"", "start":15158, "end":15396, "tags":[ "step" ], "group":"__world__", "ontologies":[ ] }, { "id":"FrhgjABcEeu5B4dnXgvb_A", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:55:08.276888+00:00", "updated":"2020-10-05T14:15:00.764415+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"my other text modificate", "prefix":"ed ratios of Buffer C (500 mM), ", "exact":"ethylene carbonate", "suffix":"", "start":15219, "end":15237, "tags":[ "reagent" ], "group":"__world__", "ontologies":[ "CHEBI" ], "settings":{ "bio_annotations":[ "" ] } }, { "id":"7Z1sugBbEeu9_wtvk1iAjw", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:53:59.317703+00:00", "updated":"2020-09-30T00:39:50.822216+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"", "prefix":"10 minutes. Wash with PBS3. Add ", "exact":"imaging buffer", "suffix":"", "start":15162, "end":15176, "tags":[ "reagent" ], "group":"__world__", "ontologies":[ "CHEBI" ], "settings":{ "bio_annotations":[ "http://purl.obolibrary.org/obo/CHEBI_35225" ] } } ] </summary>

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API filter example at 15:38. https://youtu.be/W71YZyyRPgk?t=938

Tibbles: https://blog.rstudio.com/2016/03/24/tibble-1-0-0/#:~:text=There%20are%20two%20main%20differences,to%20work%20with%20large%20data.

Gen3 Data Commons overview/explained.

GDC purpose/summary: https://youtu.be/LY5SkHJplxc?t=118

The study of whole genomes of the organisms and incorporates elements from genetics. The genomics uses a combo of DNA, DNA sequencing, and bioinformatics to sequence, assembly, and analyze the structure and the function of the genomes.

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Is GSEA really the leading method now? Not NEA?

Downloaded v4.0.9, Linux command line (legacy GLIBC, <= 2.12)

http://tandem.bu.edu/trf/trf409.legacylinux64.download.html

Used RMBlast pre-compiled binaries provided by NCBI;

Previous Release: 2.2.28

Download Pre-compiled Package: Download both the BLAST+ and RMBlast packages from NCBI for your platform:

1. RMBlast Binaries:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28

2. BLAST+ Binaries:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/

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Extract both tarballs, and symlink or copy rmblastn RMBlast to blast/bin/ location, so that all of binaries are in once-place.

recipe for merging transcripts of a gene into a single compound transcript

Broader impact for management of endangered species

Output of the project:

• analysis package written in R
• step-by-step hands-on manual
• make tools available to a broad, international community
• software made publicly available

Question: What software license will be used? The Apache software license is potentially a good choice here because it is a strong open source license supported by a wide range of communities with few obligations or barriers to access/use which supports the goal of a broad international audience.

Question: Will the data be made available under a license, as well? Maybe a CC license of some sort?

Movement types:

• land
• air
• water

Types of relocation data:

• visual observations
• GPS
• networked sensor arrays

Quantifying movement patterns at the population-level:

• migration
• range residency
• nomadism

Are there examples of this kind of data product at scale?

1) Realized mobility: Relationship of individual to population ranges. 2) Population dispersion: Spatial relationship among individuals. 3) Movement coordination: Coordination of movements among individuals. 4) Intra-individual concordance: Spatial relationship of relocations of individuals over time.

Tools gap needs to be filled to improve understanding of emergent spatial dynamics.

Movement Dynamics Homepage: http://www.clfs.umd.edu/biology/faganlab/movement/

Collaborators

• Peter Leimgruber, Smithsonian Institution
• Volker Grimm, Centre for Environmental Research - UFZ, Leipzig
• Kirk A. Olson, University of Massachusetts
• Todd K. Fuller, University of Massachusetts
• George B. Schaller, Wildlife Conservation Society
• Nuria Selva, Institute of Nature Conservation, Krakow