May 2008

IT IS SO HOT

My goodness, it has reached an incredible 99 degrees here. It's not as bad as North Carolina (HUMIDITY), but not having air conditioning means that sleeping at night semi sucks.

I wish I had a pool.

I just got something given to me in the last day that is just incredibly huge for me, and I feel super super undeserving, and now this weekend i will try to do work and live up to expectations.

And eat food.

I really worry...I think that people think I'm much more capable than I am because I really try to discuss a breadth of information. In reality , however, I feel really insecure about my capabilities to go in depth for a topic, which is what a PhD is.

Today was great. After a long day of meetings and whatnot, we went to Rick Myer's farewell bbq. I remember emailing him a long time ago to inquire into possibly working for him, only to find out that he is leaving for Huntsville Alabama, where one of my best friends Sailaja lives.

After the bbq, a few of us got together to watch grey's, and then I drove to Sarah's to pick up her and Adele. We then went to Cupertino for frozen yogurt, but ended up going into a chinese restaurant (advertised as a potsticker place, but really just another restaurant), having a second dinner, and then going to Yogurtland.

It was a festive evening. I will put up the one or two pictures I took. I'm so bad about putting them in my blog...

Job/Internships

I used to have a job blog, but that went semi defunct.

Hence, here are the latest and the greatest findings in the computational biomedical community...

Notice that the @ is replaced with AT

Genomic Health Business Development Analyst Summer Intern Description

Genomic Health, a dynamic and growing company in the personalized medicine space, is seeking a Business Development Analyst summer intern. The intern will report to the Associate Director, Business Development. Together, the intern and manager will define and implement a business relevant project, likely requiring cross-functional interactions. The intern will also be responsible for general business development support activities for the department. The intern will be required to give a final presentation at the conclusion of the project. This should be an excellent opportunity for the enthusiastic, smart candidate to develop an understanding about the business development role, and build experience in a commercial organization.

Requirements:

* Current undergraduate or masters student with an interest in life science and business
* Available approximately June through August 2008
* Excellent GPA, preferably in coursework related to biology, molecular biology, accounting, market strategy, entrepreneurship and other related curriculum.
* Excellent writer and communicator. Numerate, with ability to synthesize and analyze complex information. Very thorough and detail-oriented.

Contact: Stephanie Ogawa

sogawa AT genomichealth.com

650-569-2865

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iRhythm Technologies, Inc., a San Francsico-based medtech company founded by a former Biodesign Fellow, is offering an interesting summer internship for the summer of 2008. iRhythm is developing a novel device and software system for use in the evaluation of patients with cardiac problems. The products and systems will serve significant existing and emerging market opportunities. The position revolves around the development and refinement of the company’s primary product, which is scheduled for market introduction later this year. The culture is of the company is fast-moving, dynamic, demanding, and exciting. A seasoned management team that is geared to results will provide an excellent learning opportunity for product developers and entrepreneurs alike. iRhythm seeks an motivated and hard-working individual with good hands-on skills, who is geared towards the achievement of results. Candidates should be working towards a Bachelor of Science degree in Computer Engineering or Computer Science, Biomechanical Engineering, or Product Design.

Anticipated responsibilities will include design of components, prototyping and testing, protocol writing, and participation in various research studies. The position will require original thinking and the application of design principles in a cross-functional, multi-disciplinary environment to help develop iRhythm’s new and innovative product. iRhythm is located in the SOMA district of San Francisco, just a few blocks from CalTrain, 280, and 101.

Contact: send CV and cover letter to Uday N. Kumar, MD at uday AT irhythmtech.com

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Position Title: R&D Engineer Internship

Department: R&D

Contact: Mike Carley (Director of R&D)
Phone: 408-617-0770 x103
E-mail: mcarley AT revascular.com

Original Issue Date: 04-21-08

PURPOSE OF JOB: Use mechanical engineering and/or electrical engineering knowledge to design and develop innovative medical devices or components/subsystems in support of company’s strategic plan.

MAJOR DUTIES AND RESPONSIBILITIES:
Apply mechanical and/or electrical engineering knowledge to the design and development of medical devices.

* Solve mechanical and/or electrical engineering problems at the component through system level.
* Conduct testing utilizing existing test protocols and develop new protocols as needed.
* Generate written reports.
* Complete projects in a manner consistent with corporate objectives.
* Maintain accurate documentation of concepts, designs, drawings, and processes.
* Oversee outside vendors as required.
* Maintain QSR systems, including pre-production quality assurance procedures, pre-clinical testing programs, and post production QSR compliance in coordination with the Document Control, Clinical, and Quality Assurance functions.
* Work with other engineering, manufacturing, clinical affairs, sales and marketing, and quality assurance staff to coordinate pilot production of new products.
* Support company goals and objectives, policies and procedures, QSR, and FDA regulations.

EDUCATION REQUIREMENTS: ME or EE- Graduate or Student

EXPERIENCE REQUIREMENTS: None

OTHER QUALIFICATIONS: Working knowledge of SolidWorks is valuable.

This job description is not all inclusive. Incumbents may be required to complete other miscellaneous responsibilities as required.

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Contact:

Francisco M. De La Vega, PhD.
Scientific Fellow & Sr. Director
SOLiD Applications and Bioinformatics
Molecular and Cellular Biology R&D
Applied Biosystems
850 Lincoln Centre Dr.
Foster City, CA 94404

Tel. 1-650-638-6989
Fax. 1-650-554-2577

Bioinformatics Summer Internship
Next-Generation Sequencing Applications
Req No. 08-21133

Major Responsibilities:
The successful candidate will work on the development and
optimization of de novo DNA sequence assembly algorithms to handle
data from our next-generation, high throughput DNA sequencing
platform that generates 100s of millions of short sequencing reads
(25-50bp in length). More specifically, the project involves
adapting assembly algorithms to leverage the accuracy inherent in
the di-base reads of the SOLiD™ System. Incorporating the
information provided by paired-read libraries of different insert
sizes, and possibly small amounts of longer Sanger sequencing
reads, would be essential. The candidate will generate different
simulated data sets to test and improve the new algorithms. Working
closely with the members of the software development and
bioinformatics teams, the candidate will also test the new
algorithm implementations with real SOLiD sequencing data of small
genomes.

Skills/Knowledge Requirements:
This position requires the knowledge and skills normally acquired
through completion of a BS/BA degree in Applied Mathematics,
Computer Science, Statistics, or related field, and 1-2 years of
postgraduate training in a relevant area (e.g bioinformatics,
computational biology, MS/PhD programs). To qualify, the candidate
must have demonstrated computer-programming skills, such as C/C++/
Java and/or scripting languages (e.g. Perl, BioPerl, Phyton), and
algorithm development experience, in particular related to DNA
sequence analysis or assembly algorithms. A good understanding of
bioinformatics algorithms, sequence analysis tools, familiarity
with UNIX/Linux environment, and an appreciation of the use of
statistical methods in the interpretation of biological data are
highly desirable. Experience/good knowledge of molecular biology
and sequencing methods is a plus.

======================================

Bioinformatics Summer Internship
Next-Generation Sequencing Applications
Req No. 08-21240

Major Responsibilities:
The Position will be responsible for creating an analysis pipeline
for analysisof microbial resequencing results from the SOLiD
system. The pipeline willintegrate of the shelf components (either
already existing as part of the SOLiDAnalysis Tools, or as third
party tools). They will integrate these to create asmooth workflow
with minimal customer inputs. The final pipeline will then
bepackaged so that it can be distributed via the SOftware
community. The positionwill also create the required documentation
(in conjunction with the internaldevelopment team). The candidate
will be working with a highly motivated bioinformatics
andbiological analysis team.

Skills/Knowledge Requirements:
The candidate should be proficient in Java and scripting languages
(preferablyPERL or Python) in a UNIX environment, knowledge of
Matlab or C++ may also be ofuse.The ideal Candidate will have
software engineering skills, with previouslydemonstrated
application to biological (especially sequence based) analysis.
Anapplicant with a biological background who can demonstrate
significant softwareskills would also be considered.

Celebratory...changes?

Dinner was great--ended up being 16 people at Buca's, and then we went to fraiche afterwards. The pictures are on facebook, yay! Since it was my special day, I treated myself to...a talk. Heh, I decided to go to a talk by Martha Bulyk, who is at Harvard Systems Biology and a really great researcher/speaker. I made a total fool of myself when I interviewed with her...

I am up now, however, because i can't sleep.

I went to bed an hour ago, and instead my mind is swimming with all the things i need to do, and i'm finally getting excited about the new lab and thinking that maybe i actually have the ability to do this project. I just finished working with Atul (and wished I had gotten more done), but I know that I've gotten to know the lab (really great people) and I should move to the next project. Now I'm starting with Serafim. The computational problem and the biological problem are both completely foreign to me, so we will see how this goes. I'm so excited to learn it, however.

i played squash for the first time today with Sarah, Annie and Karen--I highly recommend it. I've never played racquetball, but it's similar. Apparently playing squash ruins your tennis game, and vice versa. So far, the only thing I can do decently is serve in squash, and my backhand kind of sucks because i'm afraid of scraping the wall. It's a great workout, though.

semi full weekend--trying to keep saturday open for getting work done, since I have a lot of stuff next week.

I'm so grateful for all the people I have met here, and the friends I have made at home and in college. It is great knowing that at 3 a.m., you can always call someone up and have a philosophical discussion that includes everything...from the serious to completely trivial matters, such as mucus.

Not that mucus is trivial.

Just saying...mucus is inherently amusing and disgusting at the same time.