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hpc seminar series

HPC Seminar Series: The Subterranean Genome of the Devil Worm

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The Subterranean Genome of the Devil Worm

Professor John R. Bracht
Department of Biology (CAS)

Abstract: The subterranean worm H. mephisto, was first discovered in a gold mine in South Africa, living nearly a mile underground in water-filled cracks in the earth’s crust. Completely isolated from the terrestrial biosphere, this organism has managed to survive, and thrive, under conditions that had been considered lethal to complex life. In this talk I will present recent data from whole-genome sequencing and analysis, and discuss how this finding sheds light on adaptive change in evolution, the limits of complex life on earth, and even on the search for life on other planets.
This talk will be geared toward a non-specialist audience.

Location: Hurst Hall, Room 203
Date/Time: October 7, 2016 at 12:00 p.m.
STATA logo

Outline for Advanced Stata Workshop

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On Friday, October 2nd, CTRL is offering it’s first ever all-day Stata training event. The workshop will go from 10:20 am to 4:45pm, with a light lunch served in the early afternoon. The full agenda for the workshop is below. Attendees do not need to be present for the entire time.

To register and see the other workshops we offer, go to http://www.american.edu/ctrl/rsgevents.cfm

 


Session 1: 10:20 -11:20 am

  • Stata basics
    • Hands-on demonstration
    • Exercise 1.1
  • Data management
    • Hands-on demonstration
    • Exercise 1.2
  • Workflow – Hands-on demonstration
  • OLS Regression Analysis
    • Hands-on demonstration
    • Exercise 1.3

Break: 11:20 – 11:30 am

Session 2: 11:30 am – 12:30 pm

  • Discrete Choice Regression Analysis
    • Hands-on demonstration
    • Exercise 2.1
  • Multinomial Regression Analysis
    • Hands-on demonstration
    • Exercise 2.2

Light Lunch: 12:30– 1:00 pm

Session 3: 1:00 -2:15 pm

  • Time Series Regression Analysis
    • Hands-on demonstration
    • Exercise 3.1.
  • Panel Data Regression Analysis
    • Hands-on demonstration
    • Exercise 3.2

Break: 2:15 – 2:25 pm

Session 4: 2:25 – 3:50 pm

  • Survey Data, Systems of Linear Regressions, GLS/FGLS/WLS
    • Hands-on demonstration
    • Exercise 3.2
  • Stata Tips and Tricks
    • Hands-on demonstration
  • Stata Programing (Simulation & Matrix)
    • Hands-on demonstration

Session 5: Question and Answers Opportunities will Follow as Desired until 5 pm

 


 

RSG Logos

New for Fall 2015! Half-day and full-day Advanced Software Training

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New! CTRL’s Research Support Group is offering extended software training sessions. For Fall 2015, we are offering full-day training in Stata and R, and half-day training in Qualtrics and NVivo. The full-day training sessions will include a light lunch.

Full descriptions for the workshops are below. If you are interested in registering to attend these, or any of our introductory or intermediate level software trainings, please register at the CTRL website: www.american.edu/ctrl/rsgevents.cfm.


 

Use of Stata for Data Management, Analysis, and Visualization
Friday, October 2nd, 10:20 am – 3:50 pm (Light lunch will be provided)
This one-day workshop offers opportunity to users, who already have some familiarity with this statistical application, to learn about a variety of advanced topics and improve their grasp on utilizing the potential of the software. Selected content will include, but is not limited to, programming with Mata, simulations, structural breaks, time series and panel data, discrete choice models, and tips and tricks in coding. Following a brief refresher on introductory aspects of Stata, the workshop will consist of about one hour allocations to discuss the topics listed above. Emphasis will be given to the coding component of working with the program and not so much to the underlying theoretical econometric principles. Register here.

Use of Qualtrics and SPSS for Survey Research and Data Analysis
Thursday, October 8th, 1:10 pm -5:15 pm
Qualtrics is a professional-level online survey software available to all AU faculty, staff, and students, and is frequently used by faculty in both research and teaching contexts. Attendees will learn the basics of online survey creation, as well as advanced methods for organizing and distributing surveys. After working on survey creation, we will explore the data analysis functions internal to Qualtrics, and show how to export survey results to SPSS and perform more sophisticated multivariate data analyses and visualization. Register here.

Use of NVivo for Qualitative Research
Thursday, October 15th, 1:10 pm – 5:15 pm
NVivo is a software tool for undertaking qualitative research that is available to all members of the AU community. We can install it on personal computers and it is also available through the Virtual Computer Lab. We plan on showing some of the basic features of NVivo in importing materials and analysis of them, but want this training to be a working session where participants bring their own qualitative data (text, audio, or video) and actually work on a project. Because there are so many different types of qualitative approaches, we want those attending to come with their own methods in mind and data particular to exploring a relevant research topic. We invite those who are thinking of attending to come by the CTRL Research Lab and get the software installed on their computer prior to the session. We can also advise on proper formatting of documents so they are easy to import into NVivo. Register here.

Use of R for Data Management, Analysis, and Visualization
Friday, November 13th, 10:20 am – 3:50 pm (Light lunch will be provided)
This is a half-day course that guides participants through the fundamentals of using R software for a typical data analysis process. Participants will learn the basics of reading data, descriptive statistics, data visualization, data analysis, and presentation of analytical results. In addition to the fundamentals, faculty may opt to learn some advanced use R techniques, such as time series, panel data, survival regression analysis, as well as utilization of R for text mining, parallel computing, visualization and analysis. Register here.

iPhone with app displayed

Mobile Tool Review: GIS Cloud Mobile Data Collection

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This Mobile Tool Review was written by Nicole Condon, CTRL Trainer and Consultant.

GIS Cloud Mobile Data Collection

Cost

Free basic service (one device and public map)
$20 premium service per device per month (private maps, better vector feature, and storage limits)

Platform

Apple App Store (iOS) and Google Play (Android) or through GISCloud.com.

What does it do?

This app allows you to gather real-time, media-enriched location information in the field. GIS Cloud Mobile Data Collection app provides a low-cost and feature-rich alternative to other geographical information system (GIS) collection services and devices. It uses the cloud to send data points and attributes directly to a custom layer on a personalized map. Access, analyze, share, and publish your data in the GIS Cloud Map Editor (available in both free and paid editions) through any web browser in real time. Features include custom form building for data collection through the mobile app and the ability to assign media (image and audio) attributes.

Which class can you use it in?

Courses that include collecting GIS or survey data in the field would find this app very useful.  It allows instant visualization and organizes data collection from multiple users, which makes collaborating on class projects very simple and fast. This is also a fantastic tool for qualitative and quantitative research data collection.

Advantages

  • Ease of use
  • Flexibility of data collection
  • Much cheaper than similar alternatives (like ArcGIS mobile collection)
  • Offline data capture allows information to be sent later
  • Instant review of maps with point data and attributes for each collection on your mobile device, including images and recorded audio
  • Images and audio attachments broaden the research potential for this tool, as a researcher can collect photographic evidence and interviews in one place
  • Data is automatically arranged into a table, which can be easily saved and imported into both ArcGIS and Google Earth

Disadvantages

  • As a relatively new app, the tool might face the growing pains associated with Beta testing
  • Utilizing all of the app’s capabilities is dependent upon each individual’s phone/tablet capabilities and data plans
  • Currently, the mobile app only allows users to create point shapes in the field. The ability to create lines and polygons should be available in 2014
  • Limited editing and spatial analysis tools.  However, importing data into another program like ArcGIS, Google Earth, or Python will solve this problem
  • Researchers that need to create private maps and larger storage need to pay a monthly fee

Overall Grade

B+ for potential use.  The next year of development for this app will be critical in determining just how effective of a tool this can be.

Additional Information

Collaborative Research using Google Drive

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The importance of peer collaboration keeps rising, for students, business, and research. Fortunately, the tools for collaboration keep improving, too.

One great tool, available to all AU community members through Google Apps for Education, is Google Drive. If you think you know Google Drive, but haven’t used it for a few months or a year, you should check it out again – Google is continually adding features to Drive products.

google drive

Google Drive is a cloud-based software and storage system that allows users to create, upload, and save documents online in multiple formats. That means you can either use it just as a storage drive, by uploading your Word documents, pictures, or many other formats, or you can create new documents using several native software formats. These include Documents, Spreadsheets, Presentations, Forms, and others. Users at American University can access Google Drive through their american.edu email account. All you need to do to collaborate using the Drive is to share your document or folder with other users and set their level of permission. If all shared users can edit, you can all work on your research at once, with no need to email multiple copies back and forth.

Here are a few of the newer features that unique to online software systems like Google Drive, rendering them great collaboration tools:

1. Research in Documents

One of the previous shortcomings of Google Docs/Drive was that it did not allow for footnotes or connection with citation programs, like EndNote. Now, using the “Research” tool located under the “Tools” menu in a Document, Google Drive allows users to search for their sources directly from the web, or from Google Scholar, and then insert that source directly as a citation. You can even select the citation format, including APA, MLA, or Chicago. It’s really one of the easiest ways to cite sources around. Plus, it allows for you to conduct and save online research directly in the document, which means that multiple users can work together in both the researching and writing stages.

research tool

2. Comments in Documents

Writing is a part of the research process, and one that’s especially hard to perform collaboratively. Microsoft Word has some useful collaborative tools such as Track Changes and Comments, but usually only one user at a time can work on the document and you have to keep track of multiple versions. In Google Documents, multiple users can make edits at the same time, and inserting comments can be a great way to communicate about the edits. If the issue in the comment has been dealt with by everyone, then the comment can be marked as “Resolved.”

Comments

3. Creating Lists in Google Spreadsheets

This is a cool feature that really takes advantage of the fact that the software is online. If you type in two related items in adjacent cells in the Spreadsheet, highlight both cells, Click on the small box in the corner of the highlighted cells, and then press CTRL while dragging the box down to later cells, Google spreadsheets will pull information from the internet to auto-fill a list based on the items you’ve entered. Excel can do this with certain items, like numeric patterns or common entries like days of the week. But Google will pull lists from Wikipedia or the CIA World Factbook, too. (Maybe it’s not as much a collaboration tool as it’s just pretty cool.)

anigif_enhanced-buzz-27983-1362612794-16(gif from http://www.buzzfeed.com/justinesharrock/a-glimpse-into-googles-brain-hidden-in-a-spreadsheet-app)

4. Google Forms

This software allows you to create custom surveys, set your fellow researchers as editors, and then email the link to your survey respondents. Once you get all of your results in, you can convert the data to spreadsheet format or export them to your preferred data analysis software. The respondents you send the survey to don’t have to be Google users, and you and your research partners get to share and save all of the results in Google Drive. The tool is meant more as a planning tool, like Doodle, but it can be used for data collection, like Survey Monkey – the advantage over these programs is that you don’t have to create and keep track of separate accounts.

form

 

That’s all we’ll cover in this post, but please, share with us what your favorite features of Google Drive are in a comment, or let us know about other online tools for collaboration!

How to Keep your Students Engaged during the Snowquester?

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cramingstudy

The American University Be Prepared site (http://www.american.edu/ctrl/preparation.cfm) gives us a few tips to keep your classes going and your students focused on the class material while campus is closed.

We invite you to view the above site and to comment to this post if you need any special support from us.  Here we summarize a few of the most handy tips:

1.  Use Blackboard to e-mail students and post announcements on readings, discussion boards or any tool you want to use to keep the class going.

2.  Meet with your students using Blackboard Collaborate tool.  You can have several students in session and do a compact class meeting.  Alternatively you can hold your office hours using Collaborate and just meet with one student at a time.  You will need a camera and a microphone if you want to have a video session with your students.  But you could simply chat with them, share your screen or use the “white board” in Collaborate to write equations or draw graphs.

Links to learning material on Collaborate can be found at the library site: http://www.american.edu/library/technology/blackboard/collaborate.cfm

3.  Film your class session using Panopto and post it in Blackboard.  We recommend making a couple of short videos (up to 15 minutes) with the key topics you want emphasized.  Remember that Spring break is next week, so the Panopto tool can help you not stay disconnected from your students for 2 weeks.  You can use Panopto to film your power point slides, your screen view and/or yourself so it can be as interactive as you want it.

Links to instructional handouts including how to get started with your first recording are available online at: http://www.american.edu/ctrl/techinclass.cfm, or through the Library’s Panopto support site: http://www.american.edu/library/technology/lecture_capture.cfm.

4.  Post your class Power Point slides in Blackboard with narration.  This is an alternative to Panopto recording for those that find it easier (we recommend Panopto though).  You can create your slides and add narration to them (remember to check your microphone settings so that the voice comes as optimal as possible).   As with Panopto recording we recommend making a couple of videos of up to 15 minutes long to optimize attention levels.

Microsoft offers step by step guides on how to add narrations to your slides: http://office.microsoft.com/en-us/powerpoint-help/record-a-voice-narration-HP005195027.aspx

Please feel free to e-mail us with questions at rsg@american.edu or to post your comments here.  We would like to know if any of these tips are useful to keep your classes going while the university remains closed.

The Snow Storm is Here…and So Are We

snowy trees

The CTRL Lab team is online ready to support you accessing the Virtual Computing Lab.  We can also help you with questions regarding SPSS and Stata.

Remember to friend us on Skype (our user name is “ctrl_research“) and send us an e-mail to rsg@american.edu if you have any questions.

For useful tips during the storm please see our post “Getting Ready for the Storm” in this link:

http://ctrlresearch.wordpress.com/2013/03/05/getting-ready-for-the-storm-how-to-stay-connected-if-au-is-closed-on-wednesday-march-6th-2013/

And remember to keep yourselves warm!

Getting ready for the storm: How to Stay Connected if AU is closed on Wednesday March 6th, 2013

polar-bear-pup

NOT TO WORRY, if the Saturn snowstorm (aka Snowquester) hits us we will be ready to support our “snowed in” AU community with Stata, SPSS and general questions.  So if we have to be closed tomorrow this is what we recommend for those wanting to connect to these and other important tools, as well as for those wishing to receive remote assistance:

1.  If you need to have a one on one consultation: Please friend us in skype (our user name is ctrl_research) or send us an e-mail to rsg@american.edu to book a skype appointment.  We can also use the Blackboard tool called “Collaborate” if we need additional ways to help you.

2.  If you need to use Stata or SPSS remotely:  Don’t let the storm stop you from finishing your project. Simply go to http://www.american.edu/vcl/ and download the Virtual Computing client (recommended option) or use it over the internet (option just recommended if for some reason you cannot download the client).  For instructions on how to use Virtual Computing go to http://www.american.edu/vcl/connect.cfm.  Please e-mail us at vcl@american.edu or rsg@american.edu if you need assistance with your Virtual Computing Lab (VCL) connection.

3.  If you need to access the J drive or your personal G drive: Go to myau.american.edu portal under the Technology option and select “Access my network drives”

4.  If you are a faculty wishing to record your class in the event the University is closed: You can use Panopto to record a session that can be uploaded to Blackboard and viewed by your students.  Links to instructional handouts including how to get started with your first recording are available online at: http://www.american.edu/ctrl/techinclass.cfm, or through the Library’s Panopto support site: http://www.american.edu/library/technology/lecture_capture.cfm.

For any questions, please add your comments to this post or e-mail us directly.

Keep Learning over Winter Break

Finals week is almost over! Congratulations on making it through another semester (students and professors!).

Enjoy your much-deserved break, but don’t let your brain atrophy and résumé stagnate. Cruising Tumblr and Facebook can only get you so far – there are plenty of ways to improve your research skills and stimulate your critical thinking skills while browsing online. Here are a few of our favorites:

1. Lynda.com

lynda

Access this learning website through your myAU portal, under the “Technology” tab. AU has paid the subscription for this fee-based service, so it’s completely free to members of the AU community. You can access thousands of videos covering hundreds of software programs. The videos are professional quality and take you step-by-step through either basic or advanced procedures in programs from Picasa to Python. By the time you complete a course, you’ll have a new resume bullet.

2. MIT OpenCourseWare

MIT

From the project’s own description: “The idea is simple: to publish all of our course materials online and make them widely available to everyone.” – Dick K.P. Yue, Professor, MIT School of Engineering. You can access the full course materials that MIT students pay big buck to take, totally free. Most classes include video lectures, syllabus, reading list, and lecture notes. Either fill in a gap in your knowledge or just pursue curiosity.

3. TED 

TED

Many of you will have already heard of this site, for good reason. The “Technology, Entertainment, Design” series of conferences invites well-known and dynamic researchers to “give the presentation of their lifetimes”. The result is often a 20-minute mind-blowing video. It’s hard to go wrong picking a TED talk. There’s also a new portion of the site called TED-Ed, which are mini-lessons prepared by educators and animated by professional animators, complete with quizzes and further resources. It’s a great way to learn without feeling like you’re learning.

4. Information is Beautiful

info

This is David McCandless’s website, filled with great examples of creative ways to display data. In our world of academic research, we see far too many ineffective and boring graphs and charts. One way to make your paper stand out is with an eye-catching and intuitive data visualization. In addition to “Information is Beautiful,” check out these tutorials from UC Berkeley’s journalism school to learn more about creating unique and effective designs.

Have a great Winter Break, and stay posted for information about CTRL’s workshops and research seminars for Spring 2013

SIS Student Quantitative Research Festival

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It’s that season again – the end of the semester! Check out some of the fascinating research conducted by SIS Graduate students, Friday November 30 from 5-7 PM in the SIS Atrium.