The Hub

The Community of Minds

  • The Hub
  • About TheCOM™
    • Testimonials
    • About The Founder: Bethany Huot
  • TheCOM Center for Educative Research™
    • Educative Research™
    • The BIOME Project
  • FAQ
  • The Whiteboard
  • Strategic Career Management (SCM)
    • SCM: Identify
    • SCM: Defining The Void
    • SCM: Commit
    • SCM: Community Perspectives
  • The Resources
    • Digital Identity Management
    • Networking & Science Communication (#SciComm)
    • Writing & Peer Review
    • Bioinformatics & Statistics
    • Methods & Technologies
    • Teaching & Learning (T&L)
      • T & L Communities
      • T & L Training Programs/Fellowships
      • T & L Career Path Prep
      • T & L Tools & Resources
    • Career Prep
    • Job Hunting
  • The Vault (Archive)
    • The File Cabinet
      • The Pub Club Files:
        • The News
        • The Pub Club
          • The Mission
          • The People
          • The Mug Club
            • The Coaster Club
          • The Python Group
          • The Publications
            • Favorite Pubs
            • Papers of Interest…
            • Scoop.it
        • 2017 Summer – Summaries & Docs
        • 2017 Spring – Summaries & Docs
        • 2016 Fall – Summaries & Docs
        • 2016 Summer – Summaries & Docs
        • 2016 Spring – Summaries & Docs
        • 2015 Fall – Summaries & Docs
        • 2015 Summer – Summaries & Docs
        • 2015 Spring – Summaries & Docs
        • 2014 Fall – Summaries & Docs

Planning Python Group 2016 (& Recaps)

  • The Pub Club (The COM)
  • The Void (The COM)
  • Training (The COM)

We created a list of topics we wanted to learn this semester:

1.     R

Working with our own data sets and stats issues as a group!! (no tutorials)

List of common statistical tests that we want to know.

“cstat” on campus speaker?

2.     Bacterial genome assemblies

Siobhan [HPCC, checking quality, alignment to a reference on a laptop]

3.     Qiime 

Nico [amplicons; bacterial and fungal communities]

4.     Python

Applications in python with relevant examples; searching, moving, isolating data using Python

iCER representative to help us? Mon, Thurs office hours (1-2pm)

 5.     GitHub!

15-20 min of refresher to get more people using this

They recently updated their user interface for uploading files instead of using command line

WEEKLY PLAN:

Google Drive document for each week that consists of:

  1.       What we want to do
  2.      What someone already knows/what they can offer
  3.       Collaboration instead of a lesson plan

We still need input from the group about specific skills in Python we want to acquire! Next week (Feb 9), we will discuss basic statistical tests and each group member will bring tests they know how to perform to share with the group. If you want to participate in the meeting and need to be added to the shared Google Drive folder or have Python input,  please contact Katie Wozniak at woznia54@msu.edu

Feb 9:

We discussed statistical tests we frequently do and what we would still like to learn. For tests we use often, we ran code on actual data sets in R to understand format of code and results of test. Still on our list to do in R: non-parametric tests, and determining homogeneity of variance before running ANOVAs. More information about the meeting and a summary can be found in the shared drive (called “Feb9Mtg: Stat Tests”).

Feb 16:

This week, we dove back into GitHub with a short tutorial (~15 minutes long). Notes on basic commands for moving files around, creating and updating branches, and updating the master can be found in the shared Google drive document called “Feb16: GitHub.” Specifically, we learned:

  1. To make changes to a document, you need a text editor (saving here would save locally to your computer).
  2. To save the changes made locally, you need Git Shell to type commands similar to those in the notes.
  3. One person has “master” rights to documents, meaning they can accept or deny any changes made in separate branches.
    1. For example: Siobhan was the master, Katie had branch A and Brian had branch B. Katie wanted to make changes to the document and Brian wanted to delete the document. Siobhan would review changes made on both branches and choose to keep branch A changes. By accepting Katie’s changes, Siobhan updated the master to be the same as what changes were made in branch A.

Apr 5:

Today we discussed processing ITS sequences using RDP (rdp.cme.msu.edu) here at MSU.  For those of you who don’t know: Internal transcribed spacer (ITS) refers to the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript. In bacteria and archaea, ITS is located between the 16S and 23S rRNA genes. On the other hand, there are two ITS’s in eukaryotes; ITS1 is located between 18S and 5.8S rRNA genes, while ITS2 is between 5.8S and 25S (in plants, or 28S in animals) rRNA genes. ITS1 corresponds to the ITS in bacteria and archaea, while ITS2 originated as an insertion that interrupted the ancestral 23S rRNA gene (Lafontane et al.)

Some of the members have had problems using RDP to identify taxonomy of sequences. Dr. Jim Cole walked us through how to use the RDP website to de-bug the problem.

Samples from: Fungi, plant, soil (either ITS 1 or 2)

Problem: RDP classifier issues through HPCC

  • The one bundled with Qiime will not work
  • Run through the website instead (rdp.cme.msu.edu) for small sets
  • Can ask questions, call, or email helpers in the RDP

Solution: Use the RDP website

  1. “Cl” for classifier
  2. Cut and paste sequences from fasta
  3. Select Fungal Warcup (or Unite)
  4. Run and see hits
  • Genera–>show assignment detail for % of matches
  • Each lineage= boot-strap confidence value (not a p value)
  • Can also do this in the command line (they have instructions online)

*The RDP website has tutorials!*

 

Share this:

  • Tweet
  • Email
  • Share on Tumblr
organization planning python group R soft skills The Void training verbal communication written communication
February 2, 2016 Katherine Wozniak

Post navigation

Plant Defense Research in the Spotlight → ← The Ethics of Genome Editing: An RCR Discussion Topic

One thought on “Planning Python Group 2016 (& Recaps)”

  1. thepubcl says:
    February 2, 2016 at 1:15 pm

    Looks like you’re off to a great start!

    Reply

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Pages

  • The Hub
  • About TheCOM™
    • Testimonials
    • About The Founder: Bethany Huot
  • TheCOM Center for Educative Research™
    • Educative Research™
    • The BIOME Project
  • FAQ
  • The Whiteboard
  • Strategic Career Management (SCM)
    • SCM: Identify
    • SCM: Defining The Void
    • SCM: Commit
    • SCM: Community Perspectives
  • The Resources
    • Digital Identity Management
    • Networking & Science Communication (#SciComm)
    • Writing & Peer Review
    • Bioinformatics & Statistics
    • Methods & Technologies
    • Teaching & Learning (T&L)
      • T & L Communities
      • T & L Training Programs/Fellowships
      • T & L Career Path Prep
      • T & L Tools & Resources
    • Career Prep
    • Job Hunting
  • The Vault (Archive)
    • The File Cabinet
      • The Pub Club Files:
        • The News
        • The Pub Club
          • The Mission
          • The People
          • The Mug Club
            • The Coaster Club
          • The Python Group
          • The Publications
            • Favorite Pubs
            • Papers of Interest…
            • Scoop.it
        • 2017 Summer – Summaries & Docs
        • 2017 Spring – Summaries & Docs
        • 2016 Fall – Summaries & Docs
        • 2016 Summer – Summaries & Docs
        • 2016 Spring – Summaries & Docs
        • 2015 Fall – Summaries & Docs
        • 2015 Summer – Summaries & Docs
        • 2015 Spring – Summaries & Docs
        • 2014 Fall – Summaries & Docs

Science / Careers Articles

Can I quote you on that? Tips to help scientists talk to the press
25 January 2021
Can I quote you on that? Tips to help scientists talk to the press

Our Experimental Error columnist offers some advice after a less-than-ideal interview [...]

My university plans to terminate my department. We’re trying to save it
21 January 2021
My university plans to terminate my department. We’re trying to save it

During precarious times, tenure isn’t a guarantee of stability, this professor learned [...]

‘This deserves our attention.’ New data highlight LGBTQ scientists’ workplace challenges
15 January 2021
‘This deserves our attention.’ New data highlight LGBTQ scientists’ workplace challenges

Researchers hope large study spurs more support for LGBTQ scientists [...]

How I talk to my science-skeptic parents about COVID-19
14 January 2021
How I talk to my science-skeptic parents about COVID-19

For this biomedical Ph.D. student, give-and-take conversations are key to communicating with her family [...]

If you’re hesitant to apply for professional awards, remember: It’s worth putting yourself forward
11 January 2021
If you’re hesitant to apply for professional awards, remember: It’s worth putting yourself forward

In this installment of Your Unicorn Career, our columnist offers guidance for overcoming four psychological blocks [...]

Benchfly / Career Development

The Trifecta: STEM, 3D Learning, and ART
22 December 2017 - Tricia Shelton
The Trifecta: STEM, 3D Learning, and ART

Equal opportunity, preparation for college and career, innovations to improve people’s lives, and a competitive US position in a global economy—- these are the needs that are driving a rethink of the approach to education.  Leading the transformation of education are initiatives like STEM and a vision for a new approach to teaching and learning […] [...]

A Changing Focus in Education
11 December 2017 - Tricia Shelton
A Changing Focus in Education

We are changemakers. We are learners. We are educators. A changing focus in education American education is in the midst of a major transformation, driven in large part, by a technology-focused global economy. Societal shifts like the Industrial Revolution had great impacts on education in the past. We can now ask ourselves, how is the […] [...]

Genetic Engineering & Biotechnology News Chooses BenchFly
9 December 2014 - Alan Marnett
Genetic Engineering & Biotechnology News Chooses BenchFly

We’re very excited to announce our new partnership with Genetic Engineering & Biotechnology News (GEN) to help bring two new video-based services to scientists. For more information, see the original release below. To learn more about how you can participate in Product Pioneers or Rising Stars of Science, please contact us at: info@benchfly.com. [...]

New Trend Alert: Using Video to Introduce Data
3 September 2014 - Emily Poulin
New Trend Alert: Using Video to Introduce Data

Here at BenchFly, we’re always looking for new ways to use video to improve scientific research. During a recent conference in Europe, the value of using video to simply introduce a research topic hit home with me. An exciting part of being a researcher of any level is the opportunity to travel to research conferences […] [...]

The ART of Video Funded by the Gates Foundation
22 August 2014 - Alan Marnett
The ART of Video Funded by the Gates Foundation

When we started BenchFly five years ago, in 2009, our mission was to make research a better career for current and future generations of scientists. Today we continue to work toward this goal using video as the primary means to educate scientists in companies, in universities and now in high schools! In the fall of 2013, we were incredibly […] [...]

copyright 2020 Bethany Huot/TheCOM,LLC / Powered by WordPress | theme SG Double
loading Cancel
Post was not sent - check your email addresses!
Email check failed, please try again
Sorry, your blog cannot share posts by email.