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文献鸟Stork是我的科研好帮手

December 17th, 2015

我在Baylor College of Medicine读研究生的时候经常遇到一种尴尬局面,就是同学们在热烈讨论本领域某篇文献的时候,我一脸茫然 — 因为我压根就不知道这篇文章。回头PubMed查查,这篇文章其实已经发表有一年了。

更绝的一个例子是,有次我老板发了文章我都不知道。当然,实验室大,有许多项目,我没有涉及那个项目。不过还是有点说不过去。

若干年后,我们开发的PaperBox的眼睛功能,现在改名为文献鸟Stork,才彻底解决了我这个问题。文献鸟用起来蛮简单的,我把能想到的所有我想跟踪的关键词和人名都输进去,然后我什么都不需要管了。文献鸟Stork会每天帮我自动搜索,把结果发送给我。现在我都是实验室第一个知道“大牛David Boas发新文章了”或者“又有人用nirs做超扫描了”等等。有面子,还长自信 :)

我有50余个关键词,文献鸟Stork会不会给我一天发50封邮件呢?不会。文献鸟Stork不会滥用你的邮箱;她会把每天的结果总结一下,最多只发一封信。

另外她还很聪明。因为有时结果多,我需要快速知道那篇文章更值得一看,文献鸟Stork就会把每篇文章对应的期刊的影响因子用颜色标记出来。颜色越黄,说明期刊越好。我在时间紧张的时候就可以只看顶尖期刊的文章了。

Stork还支持从简单到复杂的关键词。如果我想了解某个领域,比如fMRI领域,那么我就可以用一个简单的关键词fMRI即可。如果我想了解用fMRI这种方法研究情绪的文献,则我的关键词就是fMRI emotion。默认情况下,不同单词之间的关系相当于逻辑符AND,因此只要文章中同时出现了fMRI和emotion(不管顺序,也不管两个词之间有没有其它词),就会被推送。但是,如果我只想要fMRI emotion连在一起的文章,这时候加个双引号就可以了:”fMRI emotion”。

当然,更加复杂的逻辑符Stork也是支持的。比如(Nature[Journal]) AND (fMRI OR EEG) AND emotion NOT facial, 这个关键词就说明我对发表在Nature杂志上、用fMRI或者EEG(两种方法都可以)、研究情绪、但是又不包含facial这样的文献。是不是很强大?

如果对某个研究人员的文献感兴趣,可以直接用他的全名作为关键词。比如David Boas。不要加引号。当然,有的名字实在是太普通了,会有许多重名的,这时候加上他所在的单位或者城市名即可。比如David Boas, Harvard University。如果这个人可能在两个地方都工作,可以用OR,比如(Fumiko Hoeft) AND ((university of california) OR stanford)。

如果不用全名而只用简写名,就要用下面格式,姓、空格、简写。比如Reiss AL。  不要加引号,中间也不要加逗号之类的。

请大家赶快用文献鸟Stork吧,相信你会眼睛一亮的!

附录:

下面是文献鸟Stork给我发的一封信样例:

Stork Sample Email

Stork Sample Email

下面是我自己的一些关键词,做近红外或fMRI的同学们可以借鉴呢!

  1. (fumiko hoeft) AND ((university of california) OR stanford)   
  2. (jian li) AND ((phelps) OR montague OR (Peking University psychology))   
  3. baldwin Philip   
  4. brooks king-casas   
  5. cell[ta] fmri   
  6. chao liu, beijing normal university   
  7. chess stetson   
  8. David Boas   
  9. David Hong stanford   
  10. dongni yang baylor   
  11. eagleman dm [au] baylor   
  12. fmri deception   
  13. fmri resting state parent child   
  14. hanli liu, university of texas   
  15. Hosseini, S M Hadi   
  16. hyperscanning   
  17. iphone   
  18. Jack Gallant   
  19. Kendrick Kay   
  20. koniku   
  21. lumosity   
  22. montague pr [au] baylor   
  23. montague pr[au] Virginia Tech   
  24. MyConnectome   
  25. nature[ta] fmri   
  26. ning gao, tsinghua   
  27. nirs brain   
  28. nirs deception   
  29. nu zhang, washington   
  30. pearl chiu   
  31. reiss al [au] stanford   
  32. rory sayres   
  33. Russell Poldrack, stanford   
  34. saggar manish   
  35. science[ta] fmri   
  36. signe bray   
  37. smart phone brain   
  38. social nirs   
  39. stanford kesler shelli   
  40. ting ni   
  41. xianchun li, “East China Normal University”   
  42. xiaolin zhou[au] peking   
  43. xu cui AND (stanford OR baylor OR Texas)   
  44. xu q[au] harvard   
  45. yan song[au] stanford   
  46. yangming wang, peking   
  47. yufeng shen [au]   
  48. yulong li (stanford or Peking)   
  49. zen meditation   
  50. zhu chao-zhe beijing   
Author: Xu Cui Categories: brain, life, paperbox, programming, stork, web Tags:

Raspberry Pi for research labs (1)

September 30th, 2013

Raspberry Pi for research labs (3)
Raspberry Pi for research labs (2)

Raspberry Pi is a mini and incredibly cheap PC. The size is like a credit card, and the price is $35. See how small it is compared to my hand.

If you connect Pi with a TV (or monitor), a keyboard, a mouse, an internet cable, a SD card, then it becomes a full fledged PC. Pi is ideal for students to learn computer languages and other educational purposes. But many people are very creative in using Pi as a digital photo frame, a media center, a internet radio station etc. Pi’s performance is like a a 300MHz Pentium 2.

Can Pi be used in human behavior and brain imaging research labs?  Our specific goal is to see if we can integrate Pi in our Near Infrared Spectroscopy (NIRS) research. In this first part of experiment, we will see if we can get Pi running at all as a regular computer.

Joe in our lab and I rush into Fry’s to purchase some items needed to run Pi:

  1. Power adapter. Yes, Pi needs power. The adapter is actually identical to my smartphone (android) charger.
  2. SD card and reader. It is like the hard disc of a regular computer and is where data (including OS) is saved.
  3. HDMI to VGA adapter (to connect to a monitor)
  4. We already have a monitor, a USB mouse, and a USB keyboard.
1. let’s format the SD card and put OS in.
I am using a Windows computer so I follow the following instructions.
  1. Download the SD Association’s Formatting Tool from
    https://www.sdcard.org/downloads/formatter_4/eula_windows/
  2. Install and run the Formatting Tool on your machine
  3. Set “FORMAT SIZE ADJUSTMENT” option to “ON” in the “Options” menu
  4. Check that the SD card you inserted matches the one selected by the Tool
  5. Click the “Format” button
Then download NOOBS software from http://downloads.raspberrypi.org/noobs. It is a zip file, extract it and put the contents to the formatted SD card. Note, put the contents inside NOOBS_v1_3 folder to the SD card, but not the NOOBS_v1_3 folder itself.
2. Connect hardware to Pi.
Plug in the SD card to Pi, connect keyboard and mouse, HDMI to VGA adapter (then to monitor), Ethernet cable, and power adapter. As soon as you connect the power adapter, Pi will start to run. We have an option to select which OS to run, and we selected Raspbian, a version of Linux.
A close view of the hardware connected to Pi.
A far view of Pi and the keyboard/mouse, monitor etc. You can see the big juicy raspberry on the screen.
3. Surfing internet
Looks like it’s ready. Now let’s do something real - surfing internet. I opened Midori (a web browser) and can successfully go to any website I like.
Conclusions:
We successfully set up Raspberry Pi as a computer running Linux. The next step is to see if we can use it for research purpose.
Author: Xu Cui Categories: brain, linux, programming, web Tags:

Learning PaperBox in 2 minutes

September 13th, 2012

PaperBox is a cloud reference manager ideal for labs and teams to collaborate. Get it here:

http://www.peaya.com/paperbox

Author: Xu Cui Categories: technology, web Tags:

Cohort analysis

February 16th, 2011

Cohort analysis is a good metric on how users engage to an application. To do this, you:

  1. Break the users into cohorts according to when they register (bin size usually a month)
  2. Count the number of users in each cohort who login in over time
  3. Plot it

What you can get:

  1. the number of users currently using the program (read the height of period 5)
  2. retention rate over time
  3. growth rate

EverNote ECO Phil Libin used this analysis to attract investors.

Source: http://disruptivegrowth.wordpress.com/2010/07/12/running-the-numbers-cohorts/

How to make the cohort analysis plot?

It’s actually simple. Use Excel. Prepare a table where each row is one cohort over time, and each column is a time point. Then click “insert” and “Stacked Area”.

cohort plot using Excel

cohort plot using Excel

Author: Xu Cui Categories: web Tags:

Flash 3D video demo

February 5th, 2011

Racer

Ostrova

Zombie

Author: Xu Cui Categories: adobe air, programming, web Tags:

GMail Advanced Search

May 2nd, 2010

As I have quite some emails (>13000) in gmail, searching more efficiently becomes a necessity. Fortunately gmail offers some advanced search syntax.

http://mail.google.com/support/bin/answer.py?hl=en&answer=7190

  1. Search emails with attachment
    fmri meeting has:attachment
  2. Search emails with attachment, and the attachment is a pdf file
    fmri meeting filename:pdf
  3. Search emails sent from John
    fmri meeting from:john
  4. Search emails sent to John
    fmri meeting to:john
  5. Search emails sent before 2009/08/01
    fmri meeting before:2009/08/01
  6. Search emails sent after 2009/08/01
    fmri meeting after:2009/08/01
Author: Xu Cui Categories: life, web Tags:

Malicious website mimicing twitter

February 13th, 2010

You may receive a direct message from one of your friends saying:

Hi, xxx! A new twitter service! Try it, nice one! http://twltter.ru/

Don’t click the link! I clicked and it’s exactly identical to twitter’s own interface. I thought it was twitter so I entered my username/password, but nothing happened. After a few hours I realize this might be a malicious website. So I changed my twitter password.

Social networks make us more connected — but also more vulnerable for virus to spread. Be careful.

Author: Xu Cui Categories: web Tags:

Mostly used password

January 25th, 2010

The most common password is 123456, about 1% people are using it.

Mostly used password

Mostly used password

Author: Xu Cui Categories: web Tags:

Top 10 Social Networking Sites

January 21st, 2010

In terms of number of visits, Facebook takes ~50% of the US market share.

Market share of social web

Market share of social web

Author: Xu Cui Categories: web Tags:

Amf3Broker error and fix

June 27th, 2009

I encounter this error in an AIR application which uses amfphp for remoting:

The class {Amf3Broker} could not be found under the class path {/var/htdocs/amfphp/services/amfphp/Amf3Broker.php}

I googled and found several links, but their suggestions doesn’t work. I finally find the cause in the error log files of apache:

PHP Fatal error: Allowed memory size of 16777216 bytes exhausted (tried to allocate 2502231 bytes) in /var/www/html/…/amfphp2/core/amf/io/AMFBaseSerializer.php on line 98

So the cause is not amfphp, but instead my setting in php. So I edited /etc/php.ini, set memory_limit to a larger value. The problem solved.

If this doesn’t solve your problem, you may try the following links:
http://www.sephiroth.it/weblog/archives/2007/10/amfphp_and_mbstring.php
http://www.gotoandlearnforum.com/viewtopic.php?f=17&t=23708&p=109112

Author: Xu Cui Categories: adobe air, linux, php, web Tags: