Tuesday, September 28, 2010

UCSC genome

User: 'browser', password: 'genome' - full database access permissions
User: 'readonly', password: 'access' - read only access for CGI binaries.
User: 'readwrite', password: 'update' - readwrite access for hgcentral DB

Friday, September 24, 2010

Interpreting samtools flagstat output

I get the following output from running running the flagstat command in samtools for one particular bam file:

22283920 in total

0 QC failure

0 duplicates

20536595 mapped (92.16%)

22283920 paired in sequencing

11141960 read1

11141960 read2

17996862 properly paired (80.76%)

19980715 with itself and mate mapped

555880 singletons (2.49%)

852545 with mate mapped to a different chr

92547 with mate mapped to a different chr (mapQ>=5)

I am not sure what the 8th and 9th lines mean:

line 8: 17996862 properly paired (80.76%)

line 9: 19980715 with itself and mate mapped

I would have thought (looking at line 8 alone), that this means that 17996862 of the 20536595 mapped tags are "properly" (on the same chr, within the limits of the allowed insert size and same(?) orientation) paired with their mate. But I have no idea what line 9 means. Any help would be greatly appreciated!

Thanks

samtools flagstat output interpretation description
asked Jun 17 at 15:31

sasseq
16●3
One Answer: oldestnewestmost voted
2
At the risk of being overly technical, line 8, "properly paired", simply means the properly paired flag is set - it is entirely up to the program writing it to define "proper". Generally, this is set by an aligner to indicate what you describe, same chr, opposite orientation, and a within few deviations from the expected insert size. But this varies depending on the aligner used.

Line 9, means that both the forward and reverse are mapped -- somewhere, anywhere. Properly paired is a subset of these reads. You'll also find that the total of line 9 and the read pairs in which only one tag is successfully mapped (singletons) is equal to the total mapped reads. 19980715 (both mapped) + 555880 (singletons) = 20536595 (total mapped reads).

Lastly, since the sum of "proper pairs" and "itself and mate mapped to different chr" is less than "itself and mate mapped", it appears your aligner does require additional directionality or distance constraints for a "proper pair".

~J

answered Jun 22 at 10:24

jmanning2k
171●11

Thursday, September 23, 2010

trackDb

UCSC genome browser
Kent source tree

Get it here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
Or view it online: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/

Important README files: kent/src/product/README.xxx
System design

The genome browser is composed by following parts:
For service
server-side CGI binaries and HTML files
hg.conf configuration file
For administration
utility tools
.hg.conf file
data
stored in Mysql
stored in external files (optional, such as bigBed, bigWig, ...)
Design principle:
Each species will occupy a Mysql database. Inside each database:
each track correspond to one table, and each track belongs to a group
one trackDb table exists for one species, used to describe tracks
each record of the data in trackDb defines one track
one grp table to hold group info
one hgFindSpec table
Apart from databases for individual species, special databases exist:
hgFixed
hgcentral

Constructing new database

Download kent source and compile everything. See src/product/README.trackDb on how to compile everything.
Create hg.conf file at /cgi-bin/ directory. Sample file can be found at: http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/ex.hg.conf
Create .hg.conf file at your home directory:
$ cat > ~/.hg.conf
db.host=127.0.0.1
db.user=hguser
db.password=hguser
db.trackDb=trackDb
db.grp=grp
central.db=hgcentral
central.host=127.0.0.1
central.user=hguser
central.password=hguser
$ chmod 600 ~/.hg.conf
Create mysql database, make sure all folders at mysql directory are with user/grp of mysql.mysql. If not, will throw "errno: 13" when trying to modify it!!
To add new tracks:

Refer to general guide: kent/src/product/README.trackDb
generate track data in appropriate format (http://genome.ucsc.edu/FAQ/FAQformat.html)
Create a table to hold the track data. Need to identify the format of the track data file, and use corresponding loader program to load it. Following example is for bed format:
$ hgLoadBed dbName trackTableName file.bed
Realistic example: $ hgLoadBed -noBin -bedGraph=4 hg19 track_name data.bedGraph
Loader program source locates at: kent/src/hg/makeDb/
Create/update the trackDb:
Compose a new trackDb.ra file (by editing the old one) with configuration section for the new track
Example *.ra files: src/hg/makeDb/trackDb/[organism name]/[genome version]
Information on trackDb options: src/hg/makeDb/trackDb/README. Also see next section.
Compose a makefile at the place where trackDb.ra file resides. Could be like:
trackDbSql=/home/cgs/twlab/xzhou/kent/src/hg/lib/trackDb.sql
DB=hg19
all::
~/latest/hgTrackDb . ${DB} trackDb ${trackDbSql} .
Run $ make all to update the trackDb table.
Also tracks could be in bigBed or bigWig formats. See: http://www.mail-archive.com/genome@lists.soe.ucsc.edu/msg00924.html

hgsql hg19 -e 'drop table if exists myLocalBigWig; create table myLocalBigWig (fileName varchar(255) not null); insert into myLocalBigWig values ("/gbdb/hg19/bbi/myLocalBigWig.bw");'
About trackDb.ra files:

Example files for human hg19 can be found at: kent/src/hg/makeDb/trackDb/human/hg19/
use blank lines to separate tracks
each line begins with an attribute name and value, separated by space
Configurations
field: track
track trackName [override]
field: type
a lot of types there...
Track height: use maxHeightPixels 128:32:16
Track color: color r,g,b
Sub groups: subGroup1 sampleType Sample_Type fetalK=fetalK CD34=CD34 ....

Thursday, September 16, 2010

session for UCSC genomebrowser

i've enabled wiki track with sessions by these steps:
1.
Download and install mediawiki , better in a root subfolder of your mirror

2.
As written in kent/src/hg/wikiMod/README
$IP = MEDIAWIKIINSTDIR
cd kent/src/hg/wikiMod/
cp SpecialUserloginUCSC.php $IP/includes/specials/
cp SpecialUserlogouUCSC.php $IP/includes/specials/
cp configuration.SpecialUserloginUCSC.php $IP/SpecialUserloginUCSC.php
cp configuration.SpecialUserlogoutUCSC.php $IP/SpecialUserlogoutUCSC.php
cp UserloginUCSC.php $IP/includes/templates/

at the end of $IP/LocalSettings.php add these rows :

require_once( "$IP/extensions/SpecialUserloginUCSC.php" );
require_once( "$IP/extensions/SpecialUserlogoutUCSC.php" );
require_once( "$IP/includes/templates/UserloginUCSC.php" )


3.
Check if db "hgcentral" has this table: namedSessionDb.
If not use this sql to create it : CREATE TABLE namedSessionDb (
userName varchar(64) not null, # User name (from genomewiki).
sessionName varchar(255) not null, # Name that user assigns to
this session
contents longblob not null, # CGI string of var=val&... settings.
shared tinyint not null, # 1 if this session may be shared with
other users.
firstUse datetime not null, # Session creation date.
lastUse datetime not null, # Session most-recent-usage date.
useCount int not null, # Number of times this session has been
used.
settings longblob not null, # .ra-formatted metadata
#Indices
PRIMARY KEY(userName,sessionName)
);

3a.
rsync your local goldenPath/html dir with remote
htdocs/goldenPath/html/ dir.


4.
I've installed mediawiki in a subfolder of a root folder. I called it w.
Modify hg.conf adding these rows:
wiki.host=SERVER/w # w is MY installation dir of mediawiki.
wiki.userNameCookie=wikidbUserName ######### use the firebug to get the right name for wikidbUserName wikidbUserID and wikidb_session
wiki.loggedInCookie=wikidbUserID
wiki.sessionCookie=wikidb_session
wikiTrack.URL=http://SERVER/w
wikiTrack.browser=SERVER
wikiTrack.dbList=hg18,mm9,hg19

Note. If you have problem with genome session login, please check with
firefox live_http_header plugin what data is passed after login from
mediawiki. And modify wiki.userNameCookie or wiki.loggedInCookie or
wiki.sessionCookie values.

#LDAP AUTH To use ldap authentication with mediawiki download
LdapAuthentication extension from here:
cd MEDIAWIKIINSTDIR/extensions/
wget -v
http://upload.wikimedia.org/ext-dist/LdapAuthentication-trunk-r65285.tar.gz
tar xvzf LdapAuthentication-trunk-r65285.tar.gz

cd MEDIAWIKIINSTDIR

modify LocalSettings.php adding these rows (at the bottom! ) :

#enable LDAP require_once(
"$IP/extensions/LdapAuthentication/LdapAuthentication.php" );
$wgAuth = new LdapAuthenticationPlugin();

#$wgLDAPDebug = 3; //to enable ldap debug

$wgLDAPDomainNames = array( "CAMPUS" );
$wgLDAPServerNames = array( "CAMPUS" => "LDAPSERVER");
$wgLDAPSearchAttributes = array('CAMPUS' => 'uid');
$wgLDAPBaseDNs = array( "CAMPUS"=>"YOUR BASE DN" );
$wgLDAPEncryptionType = array( "CAMPUS" => "tsl" );

Add this row :
$this->mName=strtolower($this->mName);
after row 763 of SpecialUserloginUCSC.php in MEDIAWIKIDIR/includes/special/
#END LDAP AUTH

Wednesday, September 15, 2010

bwa from others

Here's what I use for bwa alignment (without removing PCR dups).
You can replace the paths with your own and put into a bash script for automation
comments or corrections welcome!

#Visit kevin-gattaca.blogspot.com to see updates of this template!
#Creates colorspace index
bwa index -a bwtsw -c hg18.fasta
#convert to fastq.gz
perl /opt/bwa-0.5.7/solid2fastq.pl Sample-input-prefix-name Sample
#aln using 4 threads
bwa aln -c -t 4 /data/public/bwa-color-index/hg18.fasta Sample.single.fastq.gz > Sample.bwa.hg18.sai
#for bwa samse
bwa samse /data/public/bwa-color-index/hg18.fasta Sample.bwa.hg18.sai Sample.single.fastq.gz > Sample.bwa.hg18.sam
#creates bam file from pre-generated .fai file
samtools view -bt /data/public/hg18.fasta.fai -o Sample.bwa.hg18.sam.bam Sample.bwa.hg18.sam
#sorts bam file
samtools sort Sample.bwa.hg18.sam.bam{,.sorted}
#From a sorted BAM alignment, raw SNP and indel calls are acquired by:
samtools pileup -vcf /data/public/bowtie-color-index/hg18.fasta Sample.bwa.hg18.sam.bam.sorted.bam > Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup
#resultant output should be further filtered by:
/opt/samtools/misc/samtools.pl varFilter Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup | awk '$6>=20' > Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup.final.pileup

bwa 4 bxd29

~/Biosoft/bwa-0.5.8a/bwa aln -c -t 8 ~/GenomeSequence/WholeGenome.fa bsd29mfrag_6_28_10_Sample1_fastq.single.fastq >bsd29mfrag_6_28_10_Sample1_fastq.sai &

~/Biosoft/bwa-0.5.8a/bwa samse ~/GenomeSequence/WholeGenome.fa bsd29mfrag_6_28_10_Sample1_fastq.sai bsd29mfrag_6_28_10_Sample1_fastq.single.fastq >bsd29mfrag_6_28_10_Sample1.sam

Saturday, September 11, 2010

writing comparison

more + noun + than

adverb:
more: significantly more; slightly more; considerably more;
less: substantially less;
as many + noun + as ... : Nearly as many as

while/however/by contrast/in comparison with/although

more to one of the ...

Tuesday, September 7, 2010

corpurus

http://xpq.blogspot.com/2007/04/blog-post.html

Saturday, September 4, 2010

stylewriter

http://sciencenet.cn/m/user_content.aspx?id=328098

英文学术论文的语言技巧

[转帖] 英文学术论文的语言技巧

a)如何指出当前研究的不足以及有目的地引导出自己的研究的重要性
通常在叙述了前人成果之后,用However来引导不足,比如
However, little information..
little attention...
little work...
little data CRS通信学社3 S3 Z3 E. V7 [$ G
little research 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, I+ R4 r* {1 U' M7 z" Y/ g7 J
or few studies 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, b0 [* H( K K7 g6 R& [
few investigations... 9 U: {- \, Z& z7 m
few researchers...
few attempts...
or no 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研3 C# I2 R! ?4 z8 P% m/ O; }
none of these studies
has (have) been less www.crs001.com, `' N7 T! y0 |& p5 z O7 H- l
done on ... 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研# S$ [& p! h2 h9 Y; _
focused on 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研; j. |! w7 _0 w" y" p! f$ d% f
attempted to CRS通信学社- ?+ O, m3 x3 s- c0 T& R
conducted
investigated 0 ~6 x- {( G. @; Q% w! [% e
studied www.crs001.com# W9 m, v6 L- |" g
(with respect to)
Previous research (studies, records) has (have)
failed to consider
ignored
misinterpreted 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研2 H7 q |0 d( M, {& J
neglected to
overestimated, underestimated
misleaded 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研# x6 h5 v2 S1 a. ^- d$ `
thus, these previous results are www.crs001.com6 T3 ~8 s8 G0 Y0 g; a' }( \+ ?
inconclusive, misleading, unsatisfactory, questionable, controversial..
Uncertainties (discrepancies) still exist ... www.crs001.com$ o) _4 K, H0 K0 Q5 D* s
这种引导一般提出一种新方法,或者一种新方向。如果研究的方法 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研) D# b! e% U* ]* z9 t5 \. Z q! J
以及方向和前人一样,可以通过下面的方式强调自己工作的作用:
However, data is still scarce 8 x; j; y2 ?# d7 j s8 h
rare www.crs001.com3 Q) c1 D5 u8 N6 g4 \/ x9 U
less accurate - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研" V1 j: V5 ]. g0 v1 F% F
there is still dearth of
We need to 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研% M0 W2 P5 @4 o: u
aim to 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研4 L5 ?, r# i( \4 Y# R$ R
have to 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研. ?- {, ]* h4 [
provide more documents
data 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研: p' I; G& W. k5 A$ ~' S4 `; k) Z
records
studies www.crs001.com9 f! m7 x0 u8 L0 s8 N+ p
increase the dataset
Further studies are still necessary... 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, E+ S5 N3 s, m
essential... 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研) t7 Z' ` M! ]. A, U' _
为了强调自己研究的重要性,一般还要在However之前介绍自己研究
问题的反方面,另一方面等等
比如: 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研" m# ~* G# F" S2 t
1)时间问题
如果你研究的问题时间上比较新,你就可以大量提及对时间较老的问题
的研究及重要性,然后说(However),对时间尺度比较新的问题研究不足
2)物性及研究手段问题 ( c5 T+ X. F7 y5 s# E
如果你要应用一种新手段或者研究方向,你可以提出当前比较流行的方法 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研) O, v0 {8 f" q4 v8 Z* n% v, W
以及物质性质,然后说对你所研究的方向和方法,研究甚少。 www.crs001.com# {$ \1 ?+ L+ F+ {$ A
3)研究区域问题
首先总结相邻区域或者其它区域的研究,然后强调这一区域研究不足
4)不确定性 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研! X. m) W& c. L: ^3 O, _
虽然前人对这一问题研究很多,但是目前有两种或者更多种的观点,
这种uncertainties, ambiguities,值得进一步澄清
5)提出自己的假设来验证 - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研1 P: n/ E" m2 ?. d' u5 h# n
如果自己的研究完全是新的,没有前人的工作进行对比,在这种情况下,
你可以自信地说,根据提出的过程,存在这种可能的结果,本文就是要
证实这种结果。
We aim to test the feasibility (reliability) of the ...
It is hoped that the question will be resolved (fall away) with our proposed www.crs001.com: M3 G0 V I$ C r. g

method (approach). - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研5 R: ?9 P9 @3 s7 G( y U
b) 提出自己的观点 - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研9 a- q7 p5 L, E/ Q
We aim to
This paper reports on - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研. @0 \8 V1 A8 O, I/ o% J+ @
provides results
extends the method..
focus on
The purpose of this paper is to 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研! E5 x0 @+ V3 j- Q) X# Q
Furthermore, Moreover, In addition,, we will also discuss... - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研 P! ^. Z- D9 `3 W* r- l9 |. f4 |
c) 圈定自己的研究范围
前言的另外一个作用就是告诉读者包括(reviewer)你的文章主要研究 - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研8 Z% Y+ U* {2 B, W+ X" t
内容。如果处理不好,reviewer会提出严厉的建议,比如你没有考虑 1 v- y* y7 D+ G: A% `9 D
某种可能性,某种研究手段等等。
为了减少这种争论,在前言的结尾你就要明确提出本文研究的范围: 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研" k8 T* K$ K4 y3 A' w5 j
1)时间尺度问题
如果你的问题涉及比较长的时序,你可以明确地提出本文只关心这 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研# e7 d- \8 O$ G3 J
一时间范围的问题。
We preliminarily focus on the older (younger)...
或者有两种时间尺度的问题 (long-term and short term),你可以说
两者都重要,但是本文只涉及其中一种
2) 研究区域的问题 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研" t. I. J+ U+ S3 ^9 i
和时间问题一样,明确提出你只关心这一地区
d) 最后的原场
在前言的最后,还可以总结性地提出,这一研究对其它研究的帮助。
或者说,further studies on ... will be summarized in our next
study (or elsewhere) www.crs001.com# x" C) m8 \$ N& v% m' g! n- D6 U
总之,其目的就是让读者把思路集中到你要讨论的问题上来。减少 CRS通信学社2 r$ u2 n8 B# ] N4 v, b2 G0 u8 S
争论(arguments).
关于词汇以及常用结构,要经常总结,多读多模仿才能融会贯通。 & x- i/ @( T- |! Y5 g
------------------------------------------------------------- CRS通信学社7 A- F1 W! `: y: n
怎样提出观点
在提出自己的观点时,采取什么样的策略很重要。
不合适的句子通常会遭到reviewer的置疑。 www.crs001.com# \5 F6 p3 C( j# a: T
1)如果观点不是这篇文章最新提出的,通常要用
We confirm that...
2)对于自己很自信的观点,可用 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研& w3 E8 l% C4 M. s* l) T) u/ [
We believe that...
3)在更通常的情况下,由数据推断出一定的结论, : Q% s: X* j: Z2 q! ?
用, Results indicate, infer, suggest, imply that... 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研* n" k& ^. g! O2 j, V3 G8 c. h' A
4) 在及其特别的情况才可以用We put forward CRS通信学社; z, ^0 ]% \6 E0 B/ G) R* F. v! K
(discover, observe..) .. "for the first time".
来强调自己的创新。 CRS通信学社) j, T) ?! R2 J$ S9 j" y+ B
5) 如果自己对所提出的观点不完全肯定,可用
We tentatively put forward (interpret this to..) 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研. {) V8 j) r* w; c8 h2 _
Or The results may be due to (caused by) attributed to 1 M. s+ f2 p. R0 ~; q# C# F
resulted from.. - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研5 _9 U6 l Y& b6 X+ L
Or This is probably a consequence of
It seems that .. can account for (interpret) this.. 3 B$ {; x* \( [& {# V, |
Or It is possible that it stem from... www.crs001.com4 T: N5 I7 W. T" [5 I' D
---------------------------------------------------------
连接词与逻辑
写英文论文最常见的一个毛病就是文章的逻辑不清楚。解决
的方法有:
1)句子上下要有连贯,不能让句子之间独立
常见的连接词语有, However, also, in addition, 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研 C* }+ v0 f* {( y# J' g* }
consequently, afterwards, moreover, Furthermore, 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研# i, ]+ B4 _. Z1 c* ?3 V! x
further, although, unlike, in contrast, Similarly,
Unfortunately, alternatively, parallel results,
In order to, despite, For example, Compared with www.crs001.com4 y% P2 E0 h. m7 G5 M5 J' h0 H
other results, thus, therefore... 0 c" K- `( c, Q, B& M( {
用好这些连接词,能够使观点表达得有层次,更加明确。
比如,如果叙述有时间顺序的事件或者文献, 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研% i( O1 \+ o* d
最早的文献可用AA advocated it for the first time. 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研7 s, L5 O% G1 N5 z: E) c t8 q
接下来,可用Then BB further demonstrated that..
再接下来,可用Afterwards, CC.. CRS通信学社% V% T, c# k- O. w8 Q5 Y' O# E7 G8 \
如果还有,可用More recent studies by DD..
如果叙述两种观点,要把它们截然分开 9 B! D. r% o+ ]) X9 n8 p% _
AA put forward that...
In contrast, BB believe
or Unlike AA, BB suggest CRS通信学社9 Q+ d4 v. H+ R9 ?1 {# [& G; I
or On the contrary (表明前面的观点错误,如果只是表明 8 e/ R6 \1 G! P* [* C! H6 M
两种对立的观点,用in contrast), BB.. 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, h! s' O1 O; Y5 N V @
如果两种观点相近,可用 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研4 v+ ]4 k5 m( I2 e* C
AA suggest
Similarly, alternatively, BB..
Or Also, BB
or BB also does ..
表示因果或者前后关系,可用
Consequently, therefore, as a result,
表明递进关系,可用furthermore, further, moreover, in addition, 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研+ W7 }1 c3 K, E4 g; J$ O
当写完一段英文,最好首先检查一下是否较好地应用 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, D/ F7 b1 C8 S' g
了这些连接词。 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研- S* B: U4 b# Z |; F% i8 `
2) 段落的整体逻辑 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研- x* M B( \: {
经常我们要叙述一个问题的几个方面。这种情况下,一定要注意 0 `4 r M! k* | c, J# c4 n$ b
逻辑结构。
首先第一段要明确告诉读者你要讨论几个部份 ( x9 f3 U- J5 s- l
...Therefore, there are three aspects of this problem have to - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研' A. ~7 B7 e! q
be addressed.
The first question involves...
The second problem relates to 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研/ w! b" F5 Z& Y- e9 W& y
The third aspect deals with... CRS通信学社1 R* U9 Q; H/ n" d9 ~$ `' l2 S
上面的例子可以清晰地把观点逐层叙述。
Or, 可以直接用First, Second, Third...Finally,..
当然,Furthermore, in addition等可以用来补充说明。
3) 讨论部份的整体结构
小标题是比较好的方法把要讨论的问题分为几个片段。
一般第一个片段指出文章最为重要的数据与结论。补充说明 CRS通信学社4 Z4 Z9 J, p3 A7 i. g# U) t" r" m
的部份可以放在最后一个片段。 www.crs001.com" w+ D% A. ?9 x% E
一定要明白文章的读者会分为多个档次。文章除了本专业
的专业人士读懂以外,一定要想办法能让更多的外专业人读懂。
所以可以把讨论部份分为两部份,一部份提出观点,另一部份 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研, {& \+ L) c- ~1 J
详细介绍过程以及论述的依据。这样专业外的人士可以了解
文章的主要观点,比较专业的讨论他可以把它当成黑箱子,而这一
部份本专业人士可以进一步研究。
为了使文章清楚,第一次提出概念时,最好加以个括弧,给出
较为详细的解释。 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研9 x$ i$ L" H! t) {( s- }+ B
如果文章用了很多的Abbreviation, 两种方法加以解决
1) 在文章最好加上个Appendix,把所有Abbreviation列表
2) 在不同的页面上,不时地给出Abbreviation的含义,用来
提醒读者。
总之,写文章的目的是要让读者读懂,读得清晰,并且采取各种 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研! V( Z; P/ a! ^8 L, E
措施方便于读者。
---------------------------------------------------------
一定要注意绝对不能全面否定前人的成果,即使在你看来 CRS通信学社; k4 f$ a ]. o& [7 D& b9 s2 Y% ^
前人的结论完全不对。这是前人工作最起码的尊重,英文 - 通信学术论坛第一站。科研,学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研9 m/ F7 g+ k3 J9 u: y) ~ S7 w7 a
叫做给别人的工作credits.
所以文章不要出现非常negative的评价,比如Their results
are wrong, very questionable, have no commonsense, etc.
遇到这类情况,可以婉转地提出: CRS通信学社! {; f0 g# @- l
Their studies may be more reasonable if they had
considered this situation.
Their results could be better convinced if they ... - E- ]8 l& K0 ]8 P5 Z6 `
Or Their conclusion may remain some uncertainties. www.crs001.com, @6 D6 ?1 L9 ]# ]
讨论部份还包括什么内容? CRS通信学社. ?$ V/ W* [8 }2 \
1. 主要数据特征的总结
2. 主要结论以及与前人观点的对比
3. 本文的不足
第三点,在一般作者看来不可取。事实上给出文章的不足恰恰
是保护自己文章的重要手段。如果刻意隐藏文章的漏洞,觉得
别人看不出来,是非常不明智的。 www.crs001.com) }* D" W [" X
所谓不足,包括以下内容:
1. 研究的问题有点片面 2 ?# T9 X' q% C6 {, g
讨论时一定要说,
It should be noted that this study has examined only..
We concentrate (focus) on only...
We have to point out that we do not.. CRS通信学社+ T1 D2 k3 E* Z* c2 p+ V
Some limitations of this study are... : U( Y; y, [: Q( `' z+ A
2. 结论有些不足
The results do not imply, 通信相关学科的论坛、图书馆、百科、知道,从事通信研究的教师、博士研究生、本科生交流的专业学术型社区。学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研5 s$ T) @ l* S) w* O r+ ]
The results can not be used to determine
be taken as evidence of www.crs001.com' L; W: Z8 v1 s: V
Unfortunately, we can not determine this from this data
Our results are lack of ...
但是,在指出这些不足之后,随后一定要再一次加强本文的重要性
以及可能采取的手段来解决这些不足,为别人或者自己的下一步 + I" H' B# A8 ?* z8 ]8 c/ {8 P
研究打下浮笔。
Notwithstanding its limitation, this study does suggest..
However, these problems could be solved if we consider 学术,论坛,百科,SCI,通信人家园,研学,通信会议,通信技术,通信工程,通信资料,通信社区,通信考研' T! S P" A9 I/ y1 d8 o
Despite its preliminary character, this study can clearly indicate..
用中文来说,这一部份是左右逢源。把审稿人想到的问题提前 www.crs001.com) } h- J! H) S9 t! ?* }
给一个交代,同时表明你已经在思考这些问题,但是由于文章
长度,试验进度或者试验手段的制约,暂时不能回答这些问题。
但是,这些通过你的一些建议,这些问题在将来的研究中有可能 www.crs001.com0 C: s: C& }$ r0 Z) T& R) e
实现。

Friday, September 3, 2010

Bioscope

http://hera.uthsc.edu:8080/bioscope/views/bioscope/BioScopeMain.faces