Frequently Asked Questions:

1. Q: How to download and use IBS 1.0 software?

A: Firstly, please visit the IBS software Page at http://ibs.biocuckoo.org/download.php. You can download the latest version of IBS software in "IBS 1.0 Download" section. Please choose the package dependent on your computer Operating System (OS). After downloading, please double clicking on the program ico, then the IBS 1.0 could be easily installed on your computer. To use the IBS 1.0 software, you can read the manual first. Also, we prepared 60 demos for you. You can browse the demos online or in local softwares.

 

2. Q: I was trying to install the software in Mac OS but my installer says the file is damaged. How can I properly install the software in Mac OS?

A: By default, Mac OS 10.8 or later only allows users to install applications from 'verified sources'. In effect, this means that users are unable to install most applications downloaded from the internet. You can follow the directions below to prevent this error message from appearing.

(1) Open the Preferences. This can be done by either clicking on the System Preferences icon in the Dock or by going to Apple Menu > System Preferences.
(2) Open the Security & Privacy pane by clicking Security & Privacy.
(3) Make sure that the General section of the the Security & Privacy pane is selected. Click the icon labeled Click the lock to prevent further changes.
(4) Enter your username and password into the prompt that appears and click Unlock.
(5) Under the section labeled Allow applications downloaded from, select Anywhere. On the prompt that appears, click Allow From Anywhere.
(6) Exit System Preferences by clicking the red button in the upper left of the window. You should now be able to install applications downloaded from the internet.

 

3. Q: What's the usage of the demos?

A: We randomly chose 60 proteins and nucleotides from the five journals. Then the protein domain graphs with motifs/functional sites are implemented in IBS 1.0. You can try to modify one of the demos into your figure at a start to use IBS 1.0.

 

4. Q: May I put two or more protein domain structures in a single graph?

A: Yes. In this new version, the IBS 1.0 was updated with several significant improvements. One of the main improvements is the support of multiple diagram representation. Now, by using IBS 1.0, you can easily draw two or more schematic diagram in a single project. If you still have special requirements for IBS, please do not hesitate to contact with us. We will realize the new functions based on experimentalists feedback in later updated versions.

 

5. Q: I have a few questions which are not listed above, how can I contact the authors of IBS 1.0?

A: Please contact the author: Dr. Jian Ren for details.

 

Supplementary materials:

    In order to estimate how many papers will contain protein domain graphs, we simply chose five typical molecular and cellular magazines, including Cell, Nature Cell Biology (NCB), The Journal of Cell Biology (JCB), Molecular Biology of the Cell (MBC) and Molecular and Cellular Biology (MCB). Then we carefully read all research articles of the five journals published in 2012 and 2013. Totally, there were 813 of 2684 articles (30.3%) to contain at least one figure for biological sequence organization (Table 1). Among those 813 articles, 415 articles (51%) presented at least one schematic diagram for nucleotide organization. Thus, we concluded that diagram of protein or nucleotide domain/motif structures in an attractive, concise and precise manner is greatly helpful for a broad readership to grasp the physiological function of a given biological sequence.

Table 1 - The schematic diagram of protein and nucleotide organization published from 2012 to 2013 were summarized for five typical molecular and cellular journals. a. Num. of Pro, the number of papers that contain at least one protein domain figure. b. Num. of Nucl, the number of papers that contain at least one nucleotide organization diagram. c. Per Nucl, the percentiles of articles with at least one nucleotide organization diagram. d. Per Pro&Nucl, the percentiles of articles with at least one protein domain graph or one nucleotide organization diagram.

Journal	Num. of Article	Num. of Proa	Num. of Nuclb	Per of Proc	Per of Pro&Nucld
CELL	680	67	99	14.56%	24.41%
NCB	229	35	43	18.78%	34.06%
JCB	473	80	59	12.47%	29.39%
MBC	658	114	90	13.68%	31.00%
MCB	644	102	124	19.25%	35.09%
Total	2684	398	415	15.46%	30.29%