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Comment: Compression by Reference (Score 1) 138

by sowalsky (#44130441) Attached to: The DNA Data Deluge

The sequence read archives (such as the one hosted by NCBI) as a repository for this sequencing data, uses "compression by reference," a highly-efficient way to compress and store a lot of the data. The raw data that comes off these sequencers is often >99% homologous to the reference genome (such as human, etc), so the most efficient way to compress and store this data is only to record what is different between the sequence output and the reference genome.

Comment: Look at the dosing! (Score 5, Insightful) 252

by sowalsky (#40994857) Attached to: Widely Used Antibacterial Chemical May Impair Muscle Function

The experiments in mice were performed at 12.5mg/kg, which would be (for the average 65-kg human) a shocking 812.5mg of Triclosan. If your standard amount of handsoap and toothpaste is 2ml that's like brushing your teeth with a 1/3 solution of triclosan and swallowing it.

Like most of the research in PNAS this was not subjected to the high level of peer review expected in most scholarly journals and this paper got through without regard to its relevance and real-world significance.

At a high enough dose, caffeine causes cancer in lab animals. But not at the doses even Slashdotters consume.

Comment: Re:Growth (Score 1) 138

by sowalsky (#39965285) Attached to: FDA Cracking Down On X-ray Exposure For Kids

While your statement is correct the cancer risk is minimal.

A typical xray is about 1-10 mrem. You get about 5 mrem of radiation dose from just an airplane ride. If a child lives in a concrete apartment building he/she will receive 100 mrem just from the radiation the concrete gives off. Annual occupational exposure limits for radiation workers are 5000 mrem. A deadly dose of radiation is about 50,000 mrem.

Comment: Go to the cloud (Score 1) 239

by sowalsky (#38242208) Attached to: Genome Researchers Have Too Much Data

For individual research units, the cost of maintaining the processing power and storage space for these types of projects can be cost-prohibitive. Cloud-based options offer distributed computing power and low-cost storage that is often a more economical solution that paying for the equipment in house, especially when genomic projects can come in spurts rather than a continuous stream.

Disclaimer: I work with large amounts of genomic data and use both in-house and cloud-based analysis tools.

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