"
-
-- date: 15. July 2019
- headline: "We imaged the doubling of shot noise due to Andreev reflections in a STM, posted 
"
-
-- date: 08. May 2019
- headline: "Irene defends her PhD!"
-
-- date: 08. May 2019
- headline: "Dome makes it on the 
"
-
-- date: 13. December 2018
- headline: "Our paper about how to construct an STM is in 
"
-
-- date: 08. October 2018
- headline: "We discovered charge trapping in a high-Tc superconductor! Publication in 
"
-
-- date: 27. September 2018
- headline: "Our MHz amplifier for STM is published in 
"
-
-- date: 16. May 2018
- headline: "Milan, Koen and Irene talk about superconductivity in 
"
-
-- date: 9. October 2017
- headline: "We contributed to Miguel and Jan's 
"
-
-- date: 17. - 21. July 2017
- headline: "Koen, Maarten and Milan will be at SCES 2017, Prague. Come check out our posters on Tuesday&Thursday and talk on Thursday!"
-
-- date: 18. June 2017
- headline: "Paper on poor electronic screening published in 
"
-
-- date: 17-18. January 2017
- headline: Irene, Koen, Maarten and Milan will be at Physics@Veldhoven 2017. (Talk at PT6.1 and poster at P9.022).
-
-- date: 25. November 2016
- headline: "We are part of a newly granted 
"
-
-- date: 12. September 2016
- headline: Koen is at Correl16, Julich.
-
-- date: 01. July 2016
- headline: Milan is at the strongly correlated electron GRC 2016.
-
-- date: 24. June 2016
- headline: Felix Baumberger is visiting.
-
-- date: 17. June 2016
- headline: Irene is at SNS2016.
-
-- date: 28. April 2016
- headline: Our results on the Mott & pseudo gap physics posted on 
"
-
-- date: 01. Jan 2016
- headline: Welcome Vitaly!
-
-- date: 17. June 2015
- headline: Welcome Kees!
-
-- date: 17. June 2015
- headline: "Maarten wins the LION image award! Check out his 
"
-
-- date: 17. June 2015
- headline: " We win a Vidi grant: 800kEUR to invest in science! (
- {{ content }}
-
-
diff --git a/_pages/aboutwebsite.md b/_pages/aboutwebsite.md
deleted file mode 100644
index bd18ba1d937..00000000000
--- a/_pages/aboutwebsite.md
+++ /dev/null
@@ -1,50 +0,0 @@
----
-title: "About the website"
-layout: textlay
-excerpt: "About the website."
-sitemap: false
-permalink: /aboutwebsite.html
----
-
-# Use this website as a template for your academic research group
-
-This website is powered by [Jekyll](https://jekyllrb.com) and uses some [Bootstrap](http://www.getbootstrap.com) and [Bootswatch](http://www.bootswatch.com). We tried to make it simple yet adaptable, so that it is easy for you to re-use it for your purpose.
-
-### Getting started
-All pages are written in [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) for easy editing, and [Jekyll](https://jekyllrb.com) uses Liquid for the data-driven pages. The publicaion list, news items, and group members are stored as `.yml` data sheets (plain text) in the `_data folder`, so that one can update the website easily. The pages are in the `_pages` folder. Updating and maintaining is easy using [Github](http://www.github.com) (not worldpress-easy, but there are other advantages (see e.g. [this](https://www.taniarascia.com/make-a-static-website-with-jekyll/), or [this](http://www.webdesignerdepot.com/2015/11/jekyll-against-the-rest-of-the-world/)). [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder.
-
-If you never used [Jekyll](https://jekyllrb.com), read the [wikipedia article](https://en.wikipedia.org/wiki/Jekyll_(software)) article and check out [their website](https://jekyllrb.com). Same for [Github](http://www.github.com), which will host your first website draft.
-
-Create and open a github account, go to [our repository](https://github.com/allanlab/allanlab), and click 'fork'. This is now your copy of the website, and you can change and adapt it as you want. You don't have to link to us or mention us (but of course we appreciate it). Then change the name of the repository to "your_username" and the name of the branch to "gh-pages". Your website is now automatically published under *your_username.github.io/your_username/*. Except that it probably still looks like our website.
-
-To modify the webpage, you can either do everything on on github.com (go to a file, click "edit", then "commit", "push"), or install [Jekyll](https://jekyllrb.com) on your computer and play with your local copy that you sync with the branch on github.com. The former is much easier in the beginning, but a bit less convenient once you start rewriting everythint. To get it to work on your computer (and to learn a bit more about [Jekyll](https://jekyllrb.com)), [here](https://www.taniarascia.com/make-a-static-website-with-jekyll/) and [here](https://scotch.io/tutorials/getting-started-with-jekyll-plus-a-free-bootstrap-3-starter-theme) are tutorials on how to use it and how set it up locally. Also, consider using the [Github desktop app](http://www.desktop.github.com), I found it helpful.
-
-### Customization
-Now let's make this *your* website.
-
-First, go to the `news.ylm`, `publist.ylm`, and `team.ylm` files in the `_data` folder and insert your own data into the data fields. Watch out: [Jekyll](https://jekyllrb.com) is quite strict about extra or missing spaces etc. Adhere to the format. In the beginning, test each change: commit, push, and check the published website.
-
-For publications, you can add a "1" in the highlight field, then it will be featured prominently. You can add important news items (red, "news1"), and less important news items (blue, "news2").
-
-For the news items, just keep adding them. The first 10 will be displayed on the 'home' page.
-
-For the `team.ylm` file
-
-Next, change the content of all files in the `_pages` folder. To change the title in the homepage, go to `homelay.html` in the `_layout` folder.
-
-Lastly, change the footer and perhaps header appropriately (in `_include`).
-
-You might also want to change the style or theme. I imported style files (in sass) from Bootstrap/Bootwatch, you can replace them with your own (in the `_sass directory`). For small changes, just work on the override stuff in the `main.sass` file in the `CSS` folder. Or change some variables in the `_variables.sass` file, like the background color etc.
-
-As said, [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder.In the end, either upload these files to your server, or buy yourself a domain and check the instructions on github on how to host it there.
-
-### Copyright / credit
-
-You can use this template as you please. You don't have to link to us or mention us (but of course we appreciate it). We also welcome it if you send us an email with a link to your website, perhaps we'll publish a list here at some point.
-
-Comments welcome.
-
-Code released under the MIT License.
-
-
-
diff --git a/_pages/allnews.md b/_pages/allnews.md
index 9a40d6fad1a..9497e088129 100644
--- a/_pages/allnews.md
+++ b/_pages/allnews.md
@@ -1,7 +1,7 @@
---
title: "News"
layout: textlay
-excerpt: "Allan Lab at Leiden University."
+excerpt: "Bonnen Lab at Indiana University."
sitemap: false
permalink: /allnews.html
---
@@ -9,6 +9,9 @@ permalink: /allnews.html
# News
{% for article in site.data.news %}
-{{ article.date }}
-{{ article.headline | markdownify}}
{{ article.date }}
{{ article.headline }}
{{ article.text}}
+{% endfor %} diff --git a/_pages/getting-started-iu-supercomputer.md b/_pages/getting-started-iu-supercomputer.md new file mode 100644 index 00000000000..1e05ef0df9a --- /dev/null +++ b/_pages/getting-started-iu-supercomputer.md @@ -0,0 +1,105 @@ +--- +title: "Vision in Action Lab - Positions" +layout: textlay +excerpt: "IU Supercomputers -- Getting Started" +sitemap: false +permalink: /resources/getting-started-iu-supercomputers +--- + +# Getting Started on IU's supercomputers + +Prerequisites: These instructions will assume that you're familiar with the material covered in [Software Carpentries Unix Shell Lesson](http://swcarpentry.github.io/shell-novice). This lesson material will cover how to use the shell to move around and manipulate files on a computer. You may also be interested in [learning some about version control](https://swcarpentry.github.io/git-novice/) as the code the lab deploys on the supercomputer is managed with git. + +## Carbonate and Big Red 3 +The lab works primarily on two of the supercomputers, Carbonate (Matlab works more readily on this one) and Big Red 3. + +## Create computing accounts. +To use Carbonate, Big Red 3 and/or Slate you will need to ["create additional computing accounts" with IU](https://access.iu.edu/Accounts/Create). Select the systems you want to create an account on and click create accounts. Provide any additional information that they request. Once you've created the accounts it will take a couple of hours for the request to be processed. Then you will be able to log-in via SSH with your IU username and password. + +Note -- We have had some difficulty with initial user accounts on this system. If after you can log-in you are unable to run a supercomputer job on slurm and it gives the following error: + + `Unable to allocate resources: Invalid account or account/partition combination specified.` + +You should reach out to the [High Performance Systems](https://mailform.kb.iu.edu/email.php?cid=26) team and describe the error. They should be able to finalize your account and resolve the issue. + +In general the HPC support folks are responsive and helpful. When you reach out to them, please always describe the problem in detail (including what system you were on, what you were trying to do, what error you received). The way to think about it is that they need to be able to reproduce the problem in order to solve it. + +## Storage +[A current overview of the storage available in conjunction with IU's supercomputers](https://kb.iu.edu/d/avkm). + +On each supercomputer you will have a home directory with an allocation of 100GB. You may also request additional storage (default 800GB and up to 1.6TB) on Slate. For projects with larger storage needs or a project with data shared across multiple users, we can request space on Slate-Project where we can request up to 15TB for free (with charges for larger storage requests). + +On the supercomputer +slate-project storage is found at: `/N/project/your-project-name`\ +slate storage is found at: `/N/slate/your-user-name` + +Current Slate-Project Accounts +| Name of slate-project partition | Description | +| ------------------------------- | ----------- | +| infant-image-statistics | Collaboration with Linda Smith's lab on XXXXXX dataset. | + + +## Using RED desktop (Graphical user interface for the supercomputer) +IU provides this tool to make the supercomputing resources more accessible to all users, particular those new to programming, computing and supercomputers. Using [RED desktop](https://kb.iu.edu/d/apum), you're able to interact with the supercomputers using a desktop interface. You will still need to [create a Carbonate account](https://access.iu.edu/Accounts/Create) using the same process I've described above. + +Once you have your Carbonate account, there are two ways to get to RED desktop. +1. [Download, install, and configure ThinLinc Client.](https://kb.iu.edu/d/aput) +2. Use your web browser and navigate to [https://red.uits.iu.edu](https://red.uits.iu.edu). If prompted, log in with your IU username and passphrase. + +Then it's like a desktop. You'll see your home directory on the desktop, as well as slurm which is the job manager. If you go up a directory, then you'll see the path of your home directory is /N/u/kbonnen/Carbonate. You can also navigate to other storage locations from here (like slate and slate-project, see [section on Storage](#storage) above. + +Note: Most of the documentation provided here will focus on using the commandline to accomplish tasks, but I suspect that almost anything can also be done from RED desktop. + + +## Accomplishing tasks on the supercomputer (Commandline interface for the supercomputer) + +### Logging in +Yay! You have an account and you're ready to go. Let's do it. + +1. Once your account is created, you can use any SSH2 client to access `bigred3.uits.iu.edu`.\ +**On a Mac or Linux machine**, open up Terminal and type the following command:\ +`ssh your-user-name@bigred3.uits.iu.edu`\ +Where your-user-name is your IU username. You will be prompted for a password. Type in your IU password.\ +\ +**On Windows** you will open up [PuTTY](https://www.putty.org/) and ssh into bigred3.uits.iu.edu with your IU username and password. + + +2. Once you've logged in with your IU username and password you will be prompted to authenticate via DUO. Follow the instructions. + +3. You should see a welcome message that looks something like this: +> Last login: Sun Apr 3 17:09:55 2022 from 149.161.198.253 +> +> Welcome to Indiana University's Big Red 3 Cluster +> Email questions and comments to hps-admin@iu.edu. +> +> For information about this cluster see https://kb.iu.edu/d/aoku. + + 4. Congratulations!! Now you should be able to navigate, manage files, etc. just like you learned in [Software Carpentries Unix Shell Lesson](http://swcarpentry.github.io/shell-novice) + +### Running your analyses as jobs on the supercomputers. + +The supercomputers rely on a job manager called slurm. In addition to the code you've written for your analysis, you'll need to create a slurm script. IU provides some guidance on how to set up and manage these scripts here: [https://kb.iu.edu/d/awrz](https://kb.iu.edu/d/awrz). Follow the instructions in the sections labeled "About job scripts" and "serial jobs" ([https://kb.iu.edu/d/awrz#scripts](https://kb.iu.edu/d/awrz#scripts)). + +- [Another example with specific instructions for running matlab jobs on the IU supercomputers.](https://kb.iu.edu/d/bdpj) The principles are largely the same for any other programming language. *Note: There may be an error in the Slurm submission script (step 2). If it doesn't work, you'll need add a line loading the matlab module during the job. Put the following line after the last line containing #SBATCH:* `module load matlab` + +- Running "batch" jobs. This is useful at times when you want to repeat a single analysis on many subjects, or perhaps on subsets of frames simultaneously. IU doesn't provide great guidance on how to do this, but Kansas does: [https://crc.ku.edu/hpc/how-to/arrays](https://crc.ku.edu/hpc/how-to/arrays). + + +### Running interactive sessions. + +Sometimes you'll want to run an interactive session. + +- [Running an interactive session in MATLAB on Carbonate.](https://kb.iu.edu/d/bdpj#run). + +- coming soon -- instructions for interactive jupyter notebook on Mac/Linux + +- [Instructions for interactive jupyter notebook on Windows.](https://blogs.iu.edu/ncgas/2021/05/07/tunneling-a-jupyter-notebook-from-an-hpc/) + +### An easier way to log-in +coming soon -- (for Mac and Linux users) + +### Using Sublime as your text editor +coming soon diff --git a/_pages/home.md b/_pages/home.md index bb0eb19ac41..40f36540152 100644 --- a/_pages/home.md +++ b/_pages/home.md @@ -1,72 +1,44 @@ --- -title: "Allan Lab - Home" +title: "Vision in Action Lab - Home" layout: homelay -excerpt: "Allan Lab at Leiden University." +excerpt: "Vision in Action Lab at Indiana University." sitemap: false permalink: / --- -We are a dynamic research group at the [Leiden Institute of Physics](http://www.physics.leidenuniv.nl). Our aim is to explore and understand [quantum materials](http://condensedconcepts.blogspot.nl/2013/05/what-is-quantum-matter.html), including strange metals, high-temperature superconductors, and quantum critical electron matter. +
+
+
+**The Vision in Action Lab**, led by [Dr. Kathryn Bonnen](/people/bonnen), studies visual perception, sensorimotor systems and the neural computations that underlie visual and sensorimotor processing. Our research relies on behavioral measurements (psychophysics, eye tracking, body motion capture) and computational modeling (of behavior, neural processing and the world). We borrow neural data from our friends and collaborators. We strive, even in our laboratory experiments, to understand the visual system and sensorimotor systems in contexts relevant to daily life (e.g., walking, balance, object tracking). In the lab we use both typical visual displays and virtual reality. Sometimes we go [hiking for science...](https://www.youtube.com/watch?v=3soholdtr7I&list=PLWxH2Ov17q5HRHVngfuMgMZn8qfOivMaf&index=1)
-
-
-
+We are located in the [School of Optometry](https://optometry.iu.edu/) at [Indiana University](https://www.indiana.edu/) and are affiliated with a number of departments and cross-disciplinary programs, including the Graduate programs in Neuroscience and Cognitive Science.
+**We are currently looking for passionate new PhD students, Postdocs, and Masters students to join the team** [(more info)]({{ site.url }}{{ site.baseurl }}/positions) **!**
-To this end, we develop novel spectroscopic-imaging scanning tunneling microscopy (SI-STM) tools to visualize the relevant quantum mechanical degrees of freedom. We want to be able to build the perfect instruments to answer the scientific questions we deem most important (see [Research](research)).
-We are located at Leiden University, the birthplace of superconductivity and home to Kamerlingh Onnes, Lorentz, Huygens, Einstein, de Sitter, and others (see e.g. [the wall of signatures from Ehrenfest lecturers](https://www.lorentz.leidenuniv.nl/history/colloquium/muur_heel.html)). We exchange ideas and work with our neighbors from [Quantum Matter & Optics](http://www.physics.leidenuniv.nl/qo-home), as well as with the colleagues from our [world-class theory section](https://www.lorentz.leidenuniv.nl).
- **We are looking for passionate new PhD students, Postdocs, and Master students to join the team** [(more info)]({{ site.url }}{{ site.baseurl }}/vacancies) **!**
+
+
-We are grateful for funding from Leiden University, [NWO](www.nwo.nl) ([Vidi talent scheme](http://www.nwo.nl/en/research-and-results/programmes/Talent+Scheme) and the [Frontiers in Nanoscience program](https://www.universiteitleiden.nl/en/research/research-projects/science/frontiers-of-nanoscience-nanofront)), and from an [ERC starting grant](https://erc.europa.eu/funding/starting-grants).
+
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diff --git a/_pages/lab-onboarding.md b/_pages/lab-onboarding.md
new file mode 100644
index 00000000000..b3031ac1385
--- /dev/null
+++ b/_pages/lab-onboarding.md
@@ -0,0 +1,64 @@
+---
+title: "Vision in Action Lab - Lab Onboarding"
+layout: textlay
+excerpt: "Lab Onboarding"
+sitemap: false
+permalink: /resources/lab-onboarding
+---
+
+# Welcome to the Vision in Action Lab!
+
+There are few things we need you to do in order to get started.
+
+
+## A. Join the Slack
+This is where we troubleshoot problems, discuss science, and manage logistics when we cannot be together in-person. If you haven't received a link, then you should ask one of your labmates (or Kate) to invite you.
+
+## B. Join the Lab Github
+We share and actively review each other's code. Don't worry if you've never used Github or git (version control) before, you will learn in lab.
+1. [Make a Github account.](https://github.com/)
+2. Share your github username with Kate so she can add you to the BonnenLab organization.
+3. If you're new to version control / git / github, you'll want to check out the Software Carpentries [Introduction to Version Control with git](https://swcarpentry.github.io/git-novice/), which might require you to first learn about the [Unix Shell](https://swcarpentry.github.io/shell-novice/). If you get stuck, ask questions!
+
+## C. IRB training
+In the lab we work with human participants and their data. To do either of these things, you will need to be approved to do so by the IU Institutional Review Board.
+
+1. Complete the IRB training entitled Biomedical Researcher, Stage 1: [Start Here](https://www.citiprogram.org/Shibboleth.sso/Login?target=https%3A%2F%2Fwww.citiprogram.org%2FSecure%2FWelcome.cfm%3finst%3d1722&entityID=https%3A%2F%2Fidp.login.iu.edu%2Fidp%2Fshibboleth)
+2. Notify Kate that you have completed the training so she can file an ammendment to have you added to her IRB.
+3. Once we're notified that the amendment is accepted, then you're official! You can now collect data or be granted access to data for analysis.
+
+## D. Add yourself to the lab website! (aka make your first BonnenLab pull request).
+I want everyone who works in lab to show up on our [Team page](https://bonnenlab.github.io/people/) on the website. In order to show up you will want to:
+1. Fork the repository -- [How to fork a repository](https://docs.github.com/en/get-started/quickstart/fork-a-repo).
+2. Add an image of yourself to the images/teampic/ folder following the first-last.jpg naming convention
+3. Add your information to the data/team_members.yml file, following the structure that you see. For example, if my name is Joanne Smith and I'm a Masters Student participating in the FADS summer program. I might put:
+
+An example:
+
+ - name: Joanne Smith
+ photo: joanne-smith.png
+ info: Masters Student -- FADS program
+ department: Data Science, Luddy School
+ link: [personal website](https://joanne-smith.com)
+
+If you don't have a personal website, you are welcome to create a personal page hosted here. Place it in the folder pages/individuals/ and then simply put the name of the .md file next to link (see Kate's, bonnen.md, for an example). You can also leave off the link if you'd prefer not to have a personal page or you want to add it later.
+
+Example without link:
+
+ - name: Joanne Smith
+ photo: joanne-smith.png
+ info: Undergraduate Research Assistant
+ department: Neuroscience
+
+Example with personal page hosted on Bonnen Lab:
+
+ - name: Joanne Smith
+ photo: joanne-smith.png
+ info: OD/MS student
+ department: Optometry
+ link: joanne-smith
+
+4. Now make a pull request and assign it to Kate for review! -- [How to make a pull request.](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request)
+
+
+## E. Read the lab manual -- COMING SOON (so you don't have to do this yet.)
diff --git a/_pages/mini_lecture_series.md b/_pages/mini_lecture_series.md
deleted file mode 100644
index 907898ff83b..00000000000
--- a/_pages/mini_lecture_series.md
+++ /dev/null
@@ -1,15 +0,0 @@
----
-title: "Allan Lab - AOA"
-layout: textlay
-excerpt: "AOA"
-sitemap: false
-permalink: /aoa.html
----
-
-# Calendar
-
-Every Tuesday at 9:30 in HL124.
-
-05.09.2017 Aarts
-
-dfghjkl
diff --git a/_pages/openings.md b/_pages/openings.md
deleted file mode 100644
index 4f215a8f80e..00000000000
--- a/_pages/openings.md
+++ /dev/null
@@ -1,42 +0,0 @@
----
-title: "Allan Lab - Vacancies"
-layout: textlay
-excerpt: "Openings"
-sitemap: false
-permalink: /vacancies
----
-
-# Open positions
-
-**Note: We currently don't have funding for additional PhD and postdoc positions. We can only welcome you if you have a fellowship. I'd be happy to support you after you apply to our group. Take a look at the [veni fellowship](https://www.nwo.nl/en/calls/nwo-talent-programme-veni-science-domain) or the Marie Curie fellowship (currently closed, next deadline probably Fall 2021, [here is last years call]({{ site.baseurl }}/downloads/h2020-wp1820-msca_en.pdf)).**
-
-
-
-
-We are always looking for new group members with passion, talent, and grit!
-
-You will have the chance to work on the grand challenges of condensed matter physics, often at the interface of instrumental design and new physics. You will be involved in determining the important and interesting questions, creating and improving instrumental setups, performing measurements, and making discoveries.
-
-### Past open positions
-
-You find the past job openings here:
-[Opening 1]({{ site.baseurl }}/downloads/GeneralPostdoc_2019_v01.pdf),
-[Opening 2]({{ site.baseurl }}/downloads/PPMS_PhD_2019_v01.pdf),
-[Opening 3]({{ site.baseurl }}/downloads/PD.pdf),
-[Opening 4]({{ site.baseurl }}/downloads/PHD1.pdf),
-[Opening 5]({{ site.baseurl }}/downloads/PHD2.pdf).
-
-### Applications for PhD and Postdoc positions
-If you are interested in working with us as a PhD student or postdoc, please send me an [email](mailto:milan.allan@gmail.com). State briefly why you are interested and attach a CV, including information about the grades you had as an undergraduate. No need for a separate cover letter or certificates. **Important**: please insert _"Application PhD"_ or _"Application Postdoc"_ in the subject line. If you are applying to a specific advertisement, note this in your email.
-
-
-### Master projects for Leiden University students
-If you are a Master student at Leiden University looking for a Master project, contact me (or any group member) per email or stop by my office.
-
-### Bsc / Master students from elsewhere
-If you are interested in pursuing a Master degree at Leiden University, see [mastersinleiden.nl](http://www.mastersinleiden.nl/programmes/physics/en/introduction). Sometimes, we take master students or summer interns if we get exceptional applicants (this usually means very good grades and a personal recommendation).
-
-
-
+
+
+
+
-Group Members
+ + **We are looking for new students and postdocs to join the team** [(see openings)]({{site.url}}{{site.baseurl}}/positions) **!** + + + + + +{% assign number_printed = 0 %} +{% for member in site.data.team_members %} + +{% assign mod = number_printed | modulo: 3 %} + +{% if mod == 0 %} +
+{% endif %}
+
+
+{% endif %}
+
+{% endfor %}
+
+
+{% if mod != 2 %}
+
+ 
+ {% if member.link != nil %}
+
{{ member.department }} + +
+
+{% assign number_printed = number_printed | plus: 1 %}
+
+{% if mod == 2 %}
+
+ {% if member.link != nil %}
+ {{ member.name }}
+ {% else %} +{{ member.name }}
+ {% endif %} + {{ member.info }}{{ member.department }} + +
-
-
-
-
-