Lab Meetings

For the Spring 2017 Semester, our meeting will be at 8:00 am every Tuesday in room 444 Moore.

Goals for the term

Learn R and R Markdown

Next Meeting: March 14, 2017

Katie’s report on Paperpile
Read and discuss (Rick, Daved, Michael leads)
- Warren, W. H. (2009). How do animals get about by vision? Visually controlled locomotion and orientation after 50 years. British Journal of Psychology, 100(S1), 277–281. https://doi.org/10.1348/000712609X414150
No meeting 2017-03-21

Spring 2017 Lab Meeting Minutes

2017-02-28
- Reports on GitHub/Databrary dataset quality check for
- Child Motion Form (MOFO)
- Child/Adult MOCO Behavior
- Read and discuss https://aeon.co/essays/how-cognitive-maps-help-animals-navigate-the-world
2017-02-21
- Updates about PLAY project demographics
- Discuss GitHub/Databrary dataset quality check for
  - Infant MOCO
  - Child Motion Form (MOFO)
  - Child/Adult MOCO Behavior
- Discuss WordBank
2017-02-07
- Katie’s report on Paperpile
  - Katie will demo its use on the RIDIR grant next week.
- Plan for using http://alias.libraries.psu.edu/ERESOURCES/PSU01568 to collect and visualize some data for the PLAY project
2017-01-31
- Watch & discuss this video: https://youtu.be/NGFO0kdbZmk
- Discuss preregistration
  - Read: Chambers, C., Munafò, M., & signatories, more than 80. (2013, June 5). Trust in science would be improved by study pre-registration. The Guardian. Retrieved from https://www.theguardian.com/science/blog/2013/jun/05/trust-in-science-study-pre-registration
  - Read: Frank, M. (2016, July 22). Preregister everything. http://babieslearninglanguage.blogspot.com/2016/07/preregister-everything.html.
2017-01-24
- Check-in on DataCamp
- Side-by-side evaluation of Zotero vs. PaperPile
- Project-by-project workflow review
- Compare to http://psu-psychology.github.io/psy-511-reproducible-research-spring-2017/in-class-activities/2017-01-23.html#22
- And to PLAY Project wiki
2017-01-17
- Read and discuss: Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Sert, N. P. du, … Ioannidis, J. P. A. (2017). A manifesto for reproducible science. Nature Human Behaviour, 1, 0021. https://doi.org/10.1038/s41562-016-0021.
  - Slides. HTML. Rmd
- Discuss plan for learning R and R Markdown using DataCamp courses.
  - Sign-up link: https://www.datacamp.com/groups/1b7b16b432bbc53dc4edfe34923406705194b3e7/invite
2017-01-10
- Attending
- Agenda
  - Complete Forms for Credit
  - Ensure all training is complete
  - This semester we will focus on learning R Markdown
    - Training Videos
    - Mini projects
    - Ultimate goal: Convert current lab website to R Markdown
Remember to check the Slack channel: http://gilmore-lab.slack.com

Fall 2016

2016-10-25
- Attending - Rick, Andrea, Amber, Alyssa, Sam, Michael O., Shivani, Michelle
- Agenda
  - Discuss figures for moco behavioral child and adult data
  - Discuss Child Study Center talk
2016-10-11
- Attending - Rick, Andrea, Amber, Daved, Michael O., Katie, Hifzah, Alyssa, Michelle
- Agenda
  - Discuss: Fesi, J.F., Thomas, A.L., & Gilmore, R.O. (2014). Cortical responses to optic flow and motion contrast across patterns and speeds. Vision Research, 100, 56–71. doi:10.1016/j.visres.2014.04.004.
  - Review draft poster for SfN 16.
- Action Items
  - Write Biography in Markdown Format for lab website - Markdown Cheatsheet
    - Incorporate at least one link and send to lab gmail account
    - Michael D., Daved, Alyssa
2016-09-27
- Attending - Rick, Andrea, Amber, Alyssa, Michael O., Hifzah, Sam
- Agenda
  - Discuss 2nd Chapter ‘An Introduction to Vision Science’: gilmore-lab/references/Palmer-1999/palmer-1999-chap-2.pdf
- Action Items
  - Everyone Read Fesi 2011 ‘Distinct cortical responses to 2D figures defined by motion contrast’ found
    - On Box: gilmore-lab/references/LabReading/Fesi2011.pdf
    - On PubMed: Distinct cortical responses to 2D figures defined by motion contrast
  - Write Biography in Markdown Format - Markdown Cheatsheet and send to lab gmail account
    - Michael D., Daved, Alyssa
  - Required Training: Complete by 9/15/2016
    Send all Certificates of Completion to the lab gmail account
    - Clery Act Training
      - Daved, Michael D., Michelle
    - Building a Safe Penn State: Reporting Child Abuse
      - Daved, Michael D., Hifzah
2016-09-13
- Attending - Rick, Andrea, Michael O., Michael D., Amber, Katie, Hifzah, Daved, Michelle, Alyssa, Shivani
- Agenda
  - Discuss 1st chapter ‘An Introduction to Vision Science’: gilmore-lab/references/Palmer-1999/palmer-1999-chap-1.pdf
- Action Items
  - Read 2nd Chapter ‘An Introduction to Vision Science’: gilmore-lab/references/Palmer-1999/palmer-1999-chap-2.pdf
  - Write Biography in Markdown Format and send to lab gmail account
  - Required Training: Complete by 9/15/2016
    Send all Certificates of Completion to the lab gmail account
    - Clery Act Training
      - Daved, Michael D., Michelle, Hifzah
    - Building a Safe Penn State: Reporting Child Abuse
      - Daved, Michael D., Hifzah
    - IRB CITI Training
      - Complete both Modules: Biomedical and Social Science
      - Hifzah
2016-08-30
- Attending - Rick, Andrea, Daved, Michael O., Sam, Shivani, Michelle, Katie, Auburn, Alyssa, Hifzah
- Agenda
  - Overview of lab meetings and projects for the semester.
  - Required Training: Complete by 9/15/2016
    Send all Certificates of Completion to the lab gmail account
    - Clery Act Training
      - Daved, Sam, Shivani, Michael D., Michelle, Alyssa, Hifzah
    - Building a Safe Penn State: Reporting Child Abuse
      - Daved, Sam, Shivani, Michael D., Alyssa, Hifzah
    - IRB CITI Training
      - Complete both Modules: Biomedical and Social Science
      - Sam, Alyssa, Hifzah
    - Watch Epilepsy Video
      - Michael D. - Need to Schedule
      - Katie, Auburn, Hifzah - Today 10:30am Room 449
      - Alyssa - Today after lab meeting Room 449
    - Background Check Completion Date
- Action Items
  - Send .pdf of completion certificates to the lab gmail account
  - Write Biography in Markdown Format and send to lab gmail account
  - Read 1st chapter ‘An Introduction to Vision Science’ - posted on box gilmore-lab/references/Palmer-1999/palmer-1999-chap-1.pdf
2016-08-23
- Attending - Daved, Michael O., Sam, Shivani, Michelle, Katie, Auburn, Alyssa, Hifzah
- Agenda
  - Introductions
    - Andrea Seisler, Lab Manager
    - Returning Lab Members
      - Daved, Michael O., Sam, Shivani, Raya, Michael D. Michelle, Karina, Katie, Auburn
    - New Lab Members: Alyssa and Hifzah
  - Highlights of active projects
    - Optic Flow
      - Infant motion coherence (MOCO) EEG - 7 more participants
      - Child motion form (MOFO) EEG - Analysis/Writing
      - Child motion form (MOCO) behavior - 1 more participant
      - Infant motion statistics
    - Symmetry
      - Adults’ sorting behavior - Analysis/Writing
    - Databrary
  - Did everyone get their background clearances completed? These are required to participate in data collection. If not, please see Elaine Prestia (140 Moore) to see what you still need.
  - Required Training: Complete by 9/15/2016 Send all Certificates of Completion to the lab gmail account
    - Clery Act Training
      - Daved, Sam, Shivani, Michael D., Michelle, Alyssa, Hifzah
    - Building a Safe Penn State: Reporting Child Abuse
      - Daved, Sam, Shivani, Michael D., Alyssa, Hifzah
    - IRB CITI Training
      - Complete both Modules: Biomedical and Social Science
      - Sam, Alyssa, Hifzah
    - Watch Epilepsy Video
      - Michael D., Karina - Need to Schedule
      - Katie, Auburn, Hifzah - 8/30 10:30am Room 449
      - Alyssa - 8/30 after lab meeting Room 449
  - If you have trouble logging in for the Clery Act or Reporting Child Abuse Training, please email learning@psu.edu to have your account reset.
  - Gather Contact information: PSU ID, PSU email, email for calendar invitations, phone
  - Lab participation
    - Volunteer or Credit?
      - If participating in lab for Credit, the psych 494 form must be signed by Dr. Gilmore and returned to the Psychology Advising Office (125 Moore) by Friday 8/26/2016 or you will be charged a late fee.
    - How many hours per week?
      - 2 credits = 6 hours
      - 3 credits = 9 hours
- Action Items
  - First students for paper assignments - Sam, Shivani, Alyssa, Hifzah
  - Interested in learning
    - coding (e.g. R, SPSS)
    - MRI data collection/analysis
    - post ideas for papers to discuss

Spring 2016

2016-03-29
- Next meeting on 2016-04-12
2016-03-22
- Agenda
  - Participants for AAC/DS project, email Emily Neumann, eeneumann3@gmail.com
  - Video coding project update
    - 8 to code; 5 complete. On moving/stationary pass.
    - Reliability coding on every 5th episode/segment.
    - Next step is pass on moving segments by locomotion type.
  - Next optic flow behavior pilot is on Friday.
  - Infant MOCO status
    - One last night. almost 8 mos. Another Friday.
  - Paper for next week? Michael and Jun will decide and post link to reference DOI.
  - Tools of the trade: git and GitHub, Markdown, Databrary, R/RStudio, Datavyu, Asana, Zotero, Box.
2016-03-15
- Debrief about optic flow behavior pilot.
  - 4 year-old. Tried new lighting bar. Camera light a distraction. Need to mask. Andrea, Katie, Corinna, Daved, Raya.
  - Button pressing difficult. Need to try pointing. Revise explanatory language and review (ARS). Change battery halfway through. Rick would like to see video of protocol.
  - Explanatory language for instructionsmoco-3pat-psychophysics-participant-instructions updated on 2016-03-15 (ars)
- Update about child MOFO analysis, and infant MOCO
  - Fesi et al 2011 and 2014 papers for image descriptions.
  - Rick and Andrea to meet at HEF to review.
- Recruiting update.
  - Making calls MTWR.
  - Are recruiters saving spreadsheet properly? Need to revise protocol and procedure for downloading and uploading spreadsheet. Will review protocol next week.
  - Excel is set up to Autosave every 5 minutes
  - Updated protocol [Phone_Call_Scheduling_Procedure] (https://github.com/gilmore-lab/protocols/blob/master/Phone_Call_Scheduling_Procedure.md) on 2016-03-16 (ars)
- Continued discussion of symmetry sorting project.
- Discuss next week.
  - Update about video coding project.
  - Assign paper for week following.
2016-02-23
- Discussion of Lee, D., & Seo, H. (2016). Neural Basis of Strategic Decision Making. Trends in Neurosciences, 39(1), 40–48. http://doi.org/10.1016/j.tins.2015.11.002. Daved, Michelle, and Michael O.
- Next week: finish symmetry sorting project update and MOFO data analysis update.
2016-02-16
- Rick discussed recent progress on symmetry sorting experiment.
2016-02-09
- Discussed
  - Plot.ly
  - ReadCube
  - ResearchGate.net
- For 2016-02-23
  - Read and discuss: Lee, D., & Seo, H. (2016). Neural Basis of Strategic Decision Making. Trends in Neurosciences, 39(1), 40–48. http://doi.org/10.1016/j.tins.2015.11.002. Daved, Michelle, and Michael O.
- Future readings could be
  - Raichle, M. E. (2009). A brief history of human brain mapping. Trends in Neurosciences, 32(2), 118–126. http://doi.org/10.1016/j.tins.2008.11.001
  - Yang, J., Kanazawa, S., Yamaguchi, M. K., & Motoyoshi, I. (2015). Pre-constancy Vision in Infants. Current Biology, 25(24), 3209–3212. http://doi.org/10.1016/j.cub.2015.10.053
2016-02-02
- Agenda
  - Innovations in Scholarly Communications Survey - Assignment: Take survey; pick two tools you aren’t familiar with and write a short paragraph about each of them.
  - Recruiting team assessment
2016-01-26
- Attending
- Agenda
  - MOCO/MOFO EEG
    - Weekly Monday 11:30-1; add to schedule
  - MOCO psychophysics child
    - Add project meeting to calendar (Andrea)
  - Symmetry sorting (Michelle)
  - Video data coding
    - Do reliability coding
    - Coders should review this site: http://dx.doi.org/10.17910/B7988V
2016-01-19
- Agenda
  - Need .md bios from some lab members
- Small Group Meeting Schedule
  - Child (MOCO) behavior - meetings 12:45-1:45 Thursdays
  - Video Coding - Meetings 10-11am Fridays or 11:15-12:15 Fridays
  - Infant motion coherence (MOCO) EEG - Everyone will participate in data collection sessions.
- Journals with articles potentially relevant to lab interests
2016-01-12
- Attending
  - Daved, Michelle, Michael O., Michael D., Jun, Sam, Shivani, Andrea
- Agenda
  - Create Schedules for project meetings
  - Psych 494 forms gathered - have Rick sign and return forms
  - Set up initial small group meetings

Fall 2015

2015-11-17
- Agenda
  - Discuss Wattam-Bell, J., Birtles, D., Nyström, P., von Hofsten, C., Rosander, K., Anker, S., … Braddick, O. (2010). Reorganization of Global Form and Motion Processing during Human Visual Development. Current Biology, 20(5), 411–415. http://doi.org/10.1016/j.cub.2009.12.020
  - Discuss Braddick, O., Atkinson, J., & Wattam-Bell, J. (2011). Chapter 6 - VERP and brain imaging for identifying levels of visual dorsal and ventral stream function in typical and preterm infants. In J. A. and G. M. I. Oliver Braddick (Ed.), Progress in Brain Research (Vol. 189, pp. 95–111). Elsevier. http://dx.doi.org/10.1016/B978-0-444-53884-0.00020-8
2015-11-10
- Agenda
  - Shivani leading discussion of Bourke, P., & Shaw, H. (2014). Spontaneous lucid dreaming frequency and waking insight. Dreaming, 24(2), 152–159. http://doi.org/10.1037/a0036908.
- Attending
  - Rick, Raya, Andrea, Jun, Shivani, Michelle, Michael, Daved
2015-10-20
- Agenda
  - Sam leads discussion of De Araujo, T. B., Silveira, F. R., Souza, D. L. S., Strey, Y. T. M., Flores, C. D., & Webster, R. S. (n.d.). Impact of video game genre on surgical skills development: a feasibility study. Journal of Surgical Research. http://doi.org/10.1016/j.jss.2015.07.035.
2015-10-13
- Agenda
  - Rick discussing Gilmore-Thomas-Fesi-2015 results, Stimuli on Databrary.
- Attending
  - Michelle, Raya, Jun, Michael, Shivani
2015-10-06
- Agenda
  - Jun leading discussion of Czerniak, S. M., Sikoglu, E. M., Navarro, A. A. L., McCafferty, J., Eisenstock, J., Stevenson, J. H., … & Moore, C. M. (2014). A resting state functional magnetic resonance imaging study of concussion in collegiate athletes. Brain imaging and behavior, 9(2), 323-332. http://dx.doi.org/10.1007/s11682-014-9312-1
- Attending
  - Daved, Michelle, Rick, Jun, Shivani, Michael, Sam
2015-09-29
- Attending
  - Michelle, Daved, Raya, Andrea, Jun
- Agenda
  - Rick presenting
September 22, 2015
- Attending
  - Michelle, Raya, Rick, Daved, Sam, Andrea, Jun, Shivani
- Agenda
  - Michelle’s presentation
  - Training status
  - Discuss paper next week, Wattam-Bell et al. (2010). http://dx.doi.org/10.1016/j.cub.2009.12.020
September 8, 2015
- New meeting location in 444 Moore
  - Must leave by 8:50a.
- Attending
  - Daved, Raya, Michelle, Rick, Michael, Sam, Shivani, Andrea
- Agenda
  - Schedules
  - Training
  - Lab mtg presentations
- Action items
  - Bios by next meeting, email to Andrea. Andrea has tutorial.
  - No lab meeting next week, Tuesday 9/15
  - Michelle will present on 9/22. Jun on 10/6. Shivani 11/10. Sam 10/20.
September 1, 2015
- Andrea will investigate (ask Elaine) moving meeting to 444 Moore.
- Introductions
  - Andrea Seisler, Lab Manager
  - Sam Pai, 3 credits 494
  - Daved Fouad
  - Raya Willoughby, 2 credits 494
  - Shivani Patel
  - Jun Oh
  - Michael O’Neill
- Highlights of active projects
  - Optic Flow
    - Infant motion coherence (MOCO) EEG
    - Child motion form (MOFO) EEG
    - Child motion form (MOCO) behavior
    - Infant motion statistics
  - Symmetry
    - Adults’ sorting behavior
  - Databrary
- Action items
  - Clery Act training (Andrea will send link).
  - Get added to psubrainlab Google calendar (send Andrea your email).
  - Register for PSYCH 494 credit.
  - Watch epilepsy video in lab.

Spring 2015

January 22, 2015
January 29, 2015
- Jun, William, Michael, Sam and Rick attended.
- Jun will lead a discussion of the following paper: Irimia, A., Goh, S.-Y. M., Torgerson, C. M., Stein, N. R., Chambers, M. C., Vespa, P. M., & Van Horn, J. D. (2013). Electroencephalographic inverse localization of brain activity in acute traumatic brain injury as a guide to surgery, monitoring and treatment. Clinical Neurology and Neurosurgery, 115(10). http://dx.doi.org/10.1016/j.clineuro.2013.08.003
- Discussed using Markdown for student bios. Markdown Help.
- Discussed logo contest.
February 5, 2015
- Jun, Michael, Shivani, Andrea, Rick
- Discussed bios on GitHub, child abuse reporting training, lab photo scheduling, epilepsy video.
February 12, 2015
- Sam, Jun, Michael, William, Shivani, Andrea, Rick
- Sam will present the following paper: Dawson, N., Morris, B. J., & Pratt, J. A. (2015). Functional brain connectivity phenotypes for schizophrenia drug discovery. Journal of Psychopharmacology, 29(2), 169–177. doi:10.1177/0269881114563635
- Rick will be out next week
February 19, 2015 - No Meeting this Week
February 26, 2015
March 5, 2015 - No Meeting this Week
March 19, 2015
March 26, 2015
April 2, 2015
April 9, 2015
April 16, 2015
April 23, 2015 - End of semester celebration at The Waffle Shop
April 30, 2015 - No Meeting!