Category: biotech

STAR-Fusion

STAR-Fusion is a program that detects RNA fusions events in RNA-Seq data. According to the paper describing the program, STAR-Fusion is much better than the dozen or so other callers under active development.

Still, reading the paper left me with some questions. As descried by the authors, STAR-Fusion is not just a good caller, but the best caller by a wide margin. See Fig 3A. The next nine best callers have AUC values of 0.5 to 0.3, but STAR-Fusion has a value of 0.8 in the author’s testing.

And what is the source of this incredible result? The authors are silent on the subject. They don’t know, or perhaps didn’t notice how remarkable their achievement is, and so don’t remark on it. The description of the STAR-Fusion algorithm seems very similar to the algorithms used by every other RNA fusion caller. Some do better than others, so details of implementation must matter.

So what is the critical advance STAR-Fusion makes? Is better sequence alignment key? Is the filtering approach? The paralog handling seems like it cuts down on false positives, is this key? Discovering the critical factors for RNA fusion calling would be an important result.

Or are the performance results in the paper dependent on the synthetic test data set the authors use? Will subsequent papers comparing STAR-Fusion to other methods find that it is only average, or sub-par?

GeneTac 1000 biochip scanner teardown

Picked up a GeneTac 1000, a biochip scanner. Here are teardown pictures:
Here is the unit:

Teardown pictures. The unit has a self-contained lamp module that plugs into the main controller unit (EG&G Optoelectronics, Model # 300mXT-04, lamp module LM-300MX). Can’t find much about it–looks to be a 300W lamp. The center of the unit has a CCD camera, a Nikon lens, and a big custom lens, and two sets of filters. The slide carousel is on the other side.

















ABI 377 Teardown

I picked up two ABI PRISM 377 DNA sequencers. These are the last generation of slab gel sequencers.
ABI 377

ABI 377

With the front open, you can see the place where the gel gets mounted.

gel door open

The left side opens, and the bottom cover comes off. The laser can be seen at the bottom, and some of the power supplies on the left.

Open cabinet

Here is the laser, a Uniphase Argon laser, 0.5W 2214-40MLA 1998.

laser
laser

The power supply modules are located on the left side. On the top left is the laser power supply. The electrophoresis power supply is on the left in the middle. To the right of it is the power distribution center–plugs for the laser and electrophoresis power supplies, and the blower motor. On the bottom at the left is the blower motor. In the middle at the bottom the top of a mirror module that bounces the laser back to the right at the level of the bottom of the gel. On the right at the bottom, the servo motor that moves the detector unit along the bottom of the gel.

left side

Here’s the laser power supply. The laser is not plugged in.
laser power supply

Close up of the laser power supply, Uniphase 2114B-40MLA 12A:
laser power supply

The power distribution center labels: J41 DC Power Supply Max 4000W J40 Heater and Pump Control

The electrophoresis power supply: Spellman P/N X2094 Rev. E4 Model No PTV5P300X2094
230V 5A, output 0-5kV, 0-60mA.

Here is a closeup of the servo: Telcomm brushless servo motor
servo

On the back side of the machine behind the top panel is this circuit board, the control, data processing, and interface board.

main board

Two interesting chips on the board, a FPGA and a pair of voltage converters.

xilinx
The FPGA is a Xilinx XC3064A

The voltage converter.
voltage converter

On the left of the main board is region with cooling lines:
pump area