Archive for December, 2018

The Great Tree of Life

Wednesday, December 19th, 2018
Cover image of The Great Tree of Life bookSoltis, D., and P. Soltis. 2018. The Great Tree of Life. Academic Press.

 

The Great Tree of Life is a concise, approachable treatment that surveys the concept of the Tree of Life, including chapters on its historical introduction and cultural connection. The Tree of Life is a metaphor used to describe the relationships between organisms, both living and extinct. It has been widely recognized that the relationship between the roughly 10 million species on earth drives the ecological system. This work covers options on how to build the tree, demonstrating its utility in drug discovery, curing disease, crop improvement, conservation biology and ecology, along with tactics on how to respond to the challenges of climate change.

This book is a key aid on the improvement of our understanding of the relationships between species, the increasing and essential awareness of biodiversity, and the power of employing modern biology to build the tree of life.

  • Provides a single reference describing the properties, history and utility of The Tree of Life
  • Introduces phylogenetics and its applications in an approachable manner
  • Written by experts on the Tree of Life
  • Includes an online companion site containing various original videos to enhance the reader’s understanding and experience

Spatial phylogenetics of Florida vascular plants: The effects of calibration and uncertainty on diversity estimates

Wednesday, December 19th, 2018
Graphical abstract of Allen et al 2018

Graphical Abstract

Allen, J. M., C. C. Germain-Aubrey, N. Barve, K. M. Neubig, L. C. Majure, S. W. Laffan, B. D. Mishler, H. L. Owens, S. A. Smith, W. M. Whitten, J. R. Abbott, D. E. Soltis, R. Guralnick, and P. S. Soltis. 2018. Spatial phylogenetics of Florida vascular plants: The effects of calibration and uncertainty on diversity estimates. iScience, doi: 10.1016/j.isci.2018.12.002.

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Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China

Wednesday, December 19th, 2018
Yang, T., L. Tedersoo, P. S. Soltis, D. E. Soltis, J. A. Gilbert, M. Sun, Y. Shi, H. Wang, Y. Li, J. Zhang, Z. Chen, H. Lin, Y. Zhao, C. Fu, and H. Chu. 2018. Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. The ISME Journal. [View on publisher’s site]

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Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum

Wednesday, December 19th, 2018
Wang, Y., W. Jiang, W. Ye, C. Fu, M. A. Gitzendanner, P. S. Soltis, D. E. Soltis, and Y. Qiu. 2018. Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum. BMC Plant Biology 18:208. [View on publisher’s site]

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Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves

Wednesday, December 19th, 2018
Hodel, R. G. J., L. L. Knowles, S. F. McDaniel, A. C. Payton, J. F. Dunaway, P. S. Soltis, and D. E. Soltis. 2018. Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves. Molecular Ecology 27:4612–4626. [View on publisher’s site]

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Research Computing accounts and storage

Monday, December 10th, 2018

Request an Account

Once you have a Gatorlink, you can request an account on the form here: https://www.rc.ufl.edu/access/account-request/

List Pam as your sponsor.

Storage

/ufrc/soltis

  • We currently have 50TB of space
    • We will can add more storage, but /ufrc storage is $140/TB/yr, so not cheap!
  • Each user has their own directory
  • The /ufrc/soltis/share/ folder can be used for sharing, common data, etc.
  • If you have important data that you need regular access to and this should be backed up, keep it in /ufrc/soltis/share/Soltis_Backup/. This is the only location on /ufrc/soltis that is backed up in any way.

/orange/soltis

  • The /orange filesystem is somewhat slower than /ufrc, so not best for active data used in running jobs.
  • We currently have 52TB of space.
  • Each user can create their own directory.
  • This is a great place to archive data you are not actively working on.
  • It is much cheaper than /ufrc–only $25/TB/yr.
  • One copy of all raw sequence data should go in /orange/soltis/SequenceBackup.
    • This folder is backed up nightly.
  • If you have important data that you do not access regularly, you can put it in /orange/soltis/Backup_and_archive

Storage Backup

As noted above, the ONLY places that are backed up in any way are:

  • /ufrc/soltis/share/Soltis_Backup/: Use for important data that you need regular access to and this should be backed up.
  • /orange/soltis/Backup_and_archive/: Use for important data that you do not access regularly.
  • /home: Research Computing does maintain a daily snapshot of your home directory for one week. See this video for accessing your snapshots.
  • /orange/soltis/SequenceBackup: For archiving raw sequence data. Should be set to read only to minimize accidental data changes.

UF and Museum VPN

Monday, December 10th, 2018

Museum VPN access

The Cisco AnyConnect VPN client can be downloaded from vpn.ufl.edu.

While you can connect with just your Gatorlink username, adding /flmnh to the end of your username will connect you to the Museum network and provide access to the Museum file server, the Geneious license server and other Museum resources.