Gorp

BioInformatics Internship Program (BIP): Building a Data Set

Thu, 16 Sep 2010 16:56:33 GMT

Congratulations on continuing as an intern in the National Institutes of Health's Bioinformatics Internship Program (BIP). As you know, you will focus on Avian Influenza (AI) work. But before embarking on that project, there are skills that you will need to know - such as how to find and compare molecular sequences and how to organize the sequences into a phylogenetic tree for evaluating their evolutionary relationship. You likely will use your influenza data set in your later work to help identify the source of an outbreak or to determine the appropriateness of a vaccine.

We have designed a set of activities to prepare you. These activities are described by your project leader in the subsequent emails. More detailed instructions for these tasks will be covered in the Requirements for these assignments.

After you complete these crucial assignments, your BIP Project Leader will introduce you to the Avian Influenza assignments.

Before you begin - be certain to explore the Background and Required Software tabs in this section.

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Subtasks for this task are:

2.1:Locating sequences in databases
2.2: Prepare a multi-sequence data set
2.3: Align multi-sequence +

BioInformatics Internship Program (BIP):Influenza Incidence

Tue, 18 Aug 2009 17:47:12 GMT

The connection between bioinformatics and public health is apparent in this next task. I'd like you to obtain data from the CDC website about the incidence of different subtypes of influenza in the U.S. human population and prepare graphs in order to identify the types of influenza that have been most prevalent during the past ten seasons.

After evaluating your graphs, be prepared to discuss the implications of your results and what the results mean in terms of predicting and in terms of developing a flu vaccine. This can be in the form of an informal report to the whole group, your fellow interns and supervisors.

Just to clarify: you and your team will gather and review influenza data from the past ten years and determine which strains should have been used for last year's vaccine. At the end, you will discuss your results, along with the challenges of predicting and developing new vaccines.

* Obtain data about the incidence of influenza in humans during the past ten years.
* Compare the incidence of infection with different strains, in different years, by graphing the data with Microsoft Excel®.
* Interpret the results and recommend a strategy with your colleagues, including:
1. Which influenza strains should have been used in preparing the vaccine for the 2006-2007 influenza season?
2. What are some issues that might have made it hard to develop a good vaccine for the 2006-2007 flu season?

See the Requirements for more detail. Some background information is given below. Have fun with this!
Background

Every spring, public health officials work with epidemiological data from Asia and other parts of the world. These data are used to identify the strains of influenza that are most prevalent in Asia and to predict which strains will be a problem in the United States during the coming season. Once strains have been identified, virologists mix these strains of influenza with other, less harmful vaccine strains, and grow the virus in fertilized chicken eggs in order to prepare the next winter's vaccine.

During the winter, when influenza circulates in the U.S., physicians are asked to report cases of influenza to the CDC (the Center for Disease Control). The CDC is the government agency responsible for tracking the causes of illness and death in the United States and for sharing this information with health care providers. Each week, statistics are published on morbidity (sickness) and mortality (death) and made available through the CDC web site to public health officials across the country.

Not only is this information about influenza cases useful for physicians and health care providers, it is useful for public health officials who need to plan for impending outbreaks and for retrospective analyses to evaluate the choices that were made in picking the viral strains used for vaccines.
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Subtasks associated with this task: None

BioInformatics Internship Program (BIP):Databases & Tools

Thu, 16 Jul 2009 19:12:07 GMT

Welcome to the Bioinformatics internship program, I am looking forward to working with each of you.

Click on Navigating the NCBI Databases in the left navigation bar of this site to start your next assignment. Your research mentor will assign you a research question that you will use the NCBI databases to answer.

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Subtasks for this task are:

1.1: Navigating the NCBI Database
1.2: Presenting Your Research

BioInformatics Internship Program (BIP):Avian Influenza

Thu, 16 Jul 2009 17:48:04 GMT

Welcome and congratulations on being an intern in the National Institutes of Healths Bioinformatics Internship Program (BIP). For this particular project, we will be working in collaboration with the World Health Organization. You will be working on a small team that is preparing to be useful when called upon later in the event of an Avian Influenza outbreak. Bioinformatics technicians or researchers are first responders of sorts - they have to take raw sequence data and determine the relationships of the circulating influenza with previously known influenzas. Your work will be critical.

The experience you have had in the previous tasks related to influenza will help you to understand and navigate through the Avian Flu data. Having done these exercises ensures that you are at the level needed do the Avian Flu related assignments in the Bioinformatics Internship Program.

Your BIP Project Leader will introduce you to the Avian Flu task, giving you specific instructions as to how to prepare your findings.

Good luck and we are glad you are here!

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Subtasks for this task are:

4.1: Aligning HA & NA Genes
4.2: Motif Analysis
4.3: Suspicious Outbreak

Innovo: Structural Collapse

Wed, 27 May 2009 00:13:52 GMT

Im pleased that we have such a talented group of interns! As you know, we have a number of high profile projects coming up. To contribute at the level we need for the search and rescue project, you will have to develop some background and expertise on structural collapse and failure.

I will give you further direction for your research and tasks in subsequent emails. Your deliverables will be detailed as well; they are just listed here:

* Presentation regarding structural collapse cases and lessons learned.
* Results and your observations of an earthquake simulation
* Excel data tables force, mechanical advantage and friction
* Presentation and write up of recommended applications of simple machines in a structural collapse situation.

Before you get started, download this handout (pdf) about documentation and project management that we have all interns read. We value keeping an engineering logbook and this will shed light on why the logbook is important!

You will have a productive internship at Innovo Engineering. Welcome!
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Subtasks associated with this task:
1.1:Causes of Structural Collapse
1.2:Challenges in Responding

Innovo: Robotics

Wed, 27 May 2009 00:10:52 GMT

Now for the fun assignment! I think you have the background you need to work directly on Innovos contract with the national rescue squad to design, build and test the performance of a robot that the rescue squad can use. Youll remember from the original briefing that the robot will need to navigate through rubble to locate people trapped in collapsed buildings and determine their status. The robot will need to either help lift or move pieces of rubble, or deliver small needed items until the rescue workers can get to them. The Robot Challenge Description (doc) describes some of the Engineering considerations in this complex task.

After examining a number of options, Innovo has partnered with Carnegie-Mellon Universitys robotics institute to use the Telepresence Robotics Kit (TeRK) as a starting model. We wanted to build on solid work already done and youll have plenty of design work to do to customize this model. I suggest that you have a look at notes from a NASA workshop on using technologies for search and rescue, and disaster assistance situations. This will help you understand some of the needs and the Engineering challenges --

http://dart2.arc.nasa.gov/Exercises/TMR2004/technology.html#robotics

Also, I think you should arrange for a meeting with one or two of our experts within Innovo to brainstorm how you might add some capabilities to your robot so it can perform search and rescue operations more effectively. I dont need to tell you about the importance of documentation to capture the ideas from your discussion. The kinds of questions and ideas your team should brainstorm:

* What types of technologies are useful in search and rescue challenges, and what features seem most useful?
* What benefits and limitations do robots have in disaster assistance?
* Ideas on how you could build and design two complementary robots that could cooperate to complete the mission successfully
* Initial planning for added robot capabilities

Id like to see the teams notes from your brainstorming session, so record the highlights. Also, do notes in your individual Engineering Logbook, so you will be able to refer to them later. Check out the Resources for important information on brainstorming and project management.

Good luck!
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Subtasks associated with this task:
2.1:Design Cycle
2.2:Design Analysis
2.3:Electrical Engineering & Computer Control
2.4:Trial, Modification, & Final Presentation

GreenHealth: Air, Water, & Food

Thu, 21 May 2009 20:06:57 GMT

I want to build on the Directors welcome and introduction to your first important work here. The research and analysis you do early on regarding use and exploitation of the earths natural resources will contribute to our later media campaigns to help others see the relationship between resource degradation and the impact on society. We want the public to be able to make informed decisions about environmental issues that affect their lives.

Youll need to be out there in the community familiarize yourself with the agencies, people and projects that will be a resource to you in investigating issues. Remember the research you do for these early assignments on regional and local issues related to air, water and food will come in handy for GreenHealths future activism..

Ive been wanting to get to this research, but I havent had time. Im really glad to have your help!

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Subtasks associated with this task:
1.1: Air Quality Research
1.2: Water Quality Research
1.3: Food & Environmental Health
1.4: Advocacy

Quicksoft Associates - Ajax

Fri, 15 May 2009 17:29:49 GMT

Im pleased to welcome the new members of the software design group.

You have been asked to work on a website for the Palo Alto Bicycle Club. By joining the development team for this project at QuickSoft Associates, you have affiliated with a talented group. We pride ourselves on bringing the best and the brightest programmers on board. This will be obvious to you when you participate in weekly code reviews during development.

We expect each of you to make the clients needs your priority and be able to communicate how we are accommodating those needs in the software you develop. QuickSoft is developing a reputation for delivering quality products on time.

Stack Up: Fraction Fundamentals

Tue, 24 Mar 2009 02:25:10 GMT

We approach the introduction of basic concepts in the representation and manipulation of fractions through a collaborative, graphical building game targeted towards 6th grade math students.

Using the multi-user input platform Mischief, the task of understanding the relationship between fractional quantities and their other numerical representations (as decimals and percents) is framed as a group activity in a shared workspace. Though the platform lends itself to a full suite of activities, the pilot activity "StackUp" will require that students construct a number of towers by role-playing a fraction and contribute to the global solution by "stacking up" their collective masses in the right combination.

Composting in Trashington

Wed, 18 Mar 2009 17:12:06 GMT

Composting in Trashington is an interactive Flash module for 6th graders to strengthen fraction concepts using compost bins. Students are put in charge of reducing the amount of trash sent to the landfills by the city of Trashington by creating and fixing compost bins using their knowledge of equivalent fractions.