2013 SCI Journal Impact Factor

Jun 22nd, 2013

2013 SCI Journal Impact Factors were released recently. http://www.bioxbio.com/if/

Actually, these are the 2012 impact factors because the impact factors cannot be calculated until all of the 2012 publications have been processed by the indexing agency. The impact factors of each year were published in next year.

The 2012 impact factor of a journal was calculated as follows:
A = the number of times that articles published in that journal in 2010 and 2011, were cited by articles in indexed journals during 2012.
B = the total number of “citable items” published by that journal in 2010 and 2011. (“Citable items” are usually articles, reviews, proceedings, or notes; not editorials or letters to the editor.)
2012 impact factor = A/B.

Bacteria, Virus, Eukaryotes genome sizes

Jul 10th, 2012

Bacteria, Virus, Eukaryotes typical genome sizes:

Virus: 1 ~ 360 kb (mimivirus: 1.2 Mb )
Bacteria: 0.5 ~ 13 Mb
Eukaryotes: 8 Mb ~ 670 Gb


Largest genome known: Polychaos dubium (670 Gb)

Human genome size: around 3,200 Mb

E.coli genome size: 4,639,221 (E. coli K-12)

Library for parsing Fasta/Fastq files using C/C++

Feb 4th, 2012

Fasta and Fastq are text-based formats for storing sequences. Parsing Fasta and Fastq is the routine work for bioinformatics researchers.

Kseq is a small and terse library for parsing the FASTA/FASTQ format. it can parse both FASTA and FASTQ format and even a mixture of FASTA and FASTQ records in one file.

Example command line for compiling a program using Kseq library:
gcc test.c -o test -lz

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R2A Medium

Nov 19th, 2010

R2A Medium (R2A Agar) is a culture medium for culturing oligographic bacteria. It is usually use to count the bacteria in drinking water treatment and distribution systerms. Here is the R2A Agar recipe:

Proteose peptone  0.5g
Casamino acids  0.5 g
Yeast extract  0.5g
Dextrose  0.5g
Soluble starch,  0.5g
Dipotassium phosphate  0.3g
Magnesium sulfate 7H2O  0.05g
Sodium pyruvate  0.3g
Agar 15g
Final pH 7.2 ± 0.2 @ 25 °C

Add ddH2O to 1000ml

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SOC Medium Recipe

Nov 15th, 2010

SOC (Super Optimal Broth) Medium is a nutrient-rich medium used for bacterial culture.

The following is SOC medium recipe for 1 L:

20g  Tryptone
5g  Yeast Extract
0.5g  NaCl
0.186g  KCl
0.952g  MgCl2
Add ddH2O to 1000ml

Adjust pH to 7.0~7.5 by adding concentrated sodium hydroxide (10N NaOH), autoclave to sterilize, add 20 ml of sterile 1 M glucose immediately before use.

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TBE Buffer Recipe

Nov 13th, 2010

Similar with TAE Buffer, TBE is also a buffer commonly used in molecular biology experimets.

5X TBE Buffer Recipe:

53 g of Tris base
27.5 g of boric acid
20 ml of 0.5 M EDTA(pH 8.0)
Add ddH2O to 1 Liter

When using, dilute the stock solution by 5x in ddH2O. (For example, adding 200ml 50X TAE Buffer to 800ml ddH2O)

Although 10X TBE Buffer can also be make as the stock solution, it much more likely precipitate than TAE. So, 5x is a better choice.

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TAE Buffer Recipe

Oct 22nd, 2010

TAE Buffer is usually used in agarose electrophoresis for the separation of nucleic acids such as DNA and RNA. The following is the TAE buffer recipe:

50X Stock Solution of TAE Buffer:

Tris base: 242g
Glacial Acetic Acid: 57.1ml
0.5 M EDTA: 100ml

Add ddH2O to 1 Liter and adjust pH to 8.5 using KOH.

1X Working Solution of TAE

1X working solution of TAE buffer is made by simply diluting the stock solution by 50x in ddH2O. (For example, adding 20ml 50X TAE Buffer to 980ml ddH2O.

See Also: TBE Buffer Recipe

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High Throughput Sequencing Platform

Oct 20th, 2010

High throughput sequencing platform, namely the second generation sequencing can produce thousands or millions of sequences in a short time with a relative low cost. Now it was widely used in metagenomic sequencing and other biological field. Currently, there are mainly 3 high throughput sequencing platform:

1. 454 pyrosequencing
GS FLX Titanium

2. Illumina (Solexa) sequencing
Illumina HiSeq 2000

3. SOLiD sequencing
The SOLiD™ System

DNA and RNA concentration Calculator

Aug 28th, 2010

The concontrations of DNA and RNA can be calculated by measuring their optical density (OD260), and the purity of these nucleic acids can be estimated by the ratio of OD260 to OD280. The following is a Nucleic Acids Calculator, The concentrations of dsDNA, ssDNA, RNA, ssOligo can be calculated easily.
Read more…

SCI Journal Impact Factor

Aug 8th, 2010

SCI Journal Impact Factor Query
The query function is coming soon….

SCI Journal Impact Factor (IF) is a measure reflecting the average number of citations to articles published in science and social science journals. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. via Wikipedia