Searching SRA
bio
has support to automatically query your data for additional information at sra.
While Not all GenBank records are properly cross referenced, but for those that are bio
can get you the SRA inforamation right away. Here is how it works. Get a strain of Ebola sequenced in 2014
bio KM233118 --fetch --rename ebola
First check to see if the record is being properly cross referenced:
bio ebola --sra
ebola BioProject PRJNA257197
ebola BioSample SAMN02952049
We can see that the data has both a BioProject and a BioSample associated with it. It means we may obtained a more the detailed information on the sequencing data that produced the information:
bio ebola --sra --sample | head -38
[
{
"Run": "SRR1553609",
"ReleaseDate": "2014-08-19 11:41:53",
"LoadDate": "2014-08-19 11:18:49",
"spots": "464802",
"bases": "93890004",
"spots_with_mates": "464802",
"avgLength": "202",
"size_MB": "51",
"download_path": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1553609/SRR1553609.1",
"Experiment": "SRX674271",
"LibraryName": "NM042.3.FCH9",
"LibraryStrategy": "RNA-Seq",
"LibrarySelection": "cDNA",
"LibrarySource": "TRANSCRIPTOMIC",
"LibraryLayout": "PAIRED",
"InsertSize": "0",
"InsertDev": "0",
"Platform": "ILLUMINA",
"Model": "Illumina HiSeq 2500",
"SRAStudy": "SRP045416",
"BioProject": "PRJNA257197",
"Study_Pubmed_id": "2",
"ProjectID": "257197",
"Sample": "SRS677968",
"BioSample": "SAMN02952049",
"SampleType": "simple",
"TaxID": "186538",
"ScientificName": "Zaire ebolavirus",
"SampleName": "NM042.3",
"Tumor": "no",
"CenterName": "BI",
"Submission": "SRA178666",
"Consent": "public",
"RunHash": "9D6BFED60C2E1DAB6CC06BE718DDA1C0",
"ReadHash": "B783CD0B858C0BED5FF3BC7319CAFF19"
},
We can also obtain the full run information for the entire project (we are limiting the results to make the query speedier):
bio ebola --sra --project --limit 10 | head -10
[
{
"Run": "SRR1972967",
"ReleaseDate": "2015-04-14 13:52:35",
"LoadDate": "2015-04-14 13:47:37",
"spots": "1013114",
"bases": "204649028",
"spots_with_mates": "1013114",
"avgLength": "202",
"size_MB": "114",
You can also produce the output in a tab delimited format:
bio ebola --sra --project --table --limit 10 | cut -f 1,5,8,12,15,19,29 | head
Run bases size_MB LibraryStrategy LibraryLayout Model SampleName
SRR1972967 204649028 114 RNA-Seq PAIRED Illumina HiSeq 2500 G6062.1
SRR1972968 168524560 94 RNA-Seq PAIRED Illumina HiSeq 2500 G6069.1
SRR1972969 123767824 66 RNA-Seq PAIRED Illumina HiSeq 2500 G6089.1
SRR1972970 103654482 56 RNA-Seq PAIRED Illumina HiSeq 2500 G6091.1
SRR1972971 102959602 59 RNA-Seq PAIRED Illumina HiSeq 2500 G6095.1
SRR1972972 92415808 52 RNA-Seq PAIRED Illumina HiSeq 2500 G6103.1
SRR1972973 82751118 45 RNA-Seq PAIRED Illumina HiSeq 2500 G6104.1
SRR1972974<PHONE_NUMBER> 572 RNA-Seq PAIRED Illumina HiSeq 2500 W218.0
SRR1972975 546366570 292 RNA-Seq PAIRED Illumina HiSeq 2500 W219.0


If Apple holds the future of Computing ,I dont want to be a developer
Software development is my childhood dream. I always wanted to be computer engineer and now i am very close to it . Only two months away from my computer degree .
But suddenly a question pop ups in my mind “ Do i really want to be a developer of the future? “ .After seeing current dynamics of industry, my answer seems to be no !!! . Let me explain.
###Openness and Choice
The primary things drew me to the software field is its openness and choice. Software industry became very open ,thanks to open source movement and Internet. Its open in terms of code,process,entrepreneurship etc . There are millions of books,sites,blogs to help you in every step of journey . There are many experts to help you when you encounter a problem . We call this expert group as the community.
Software field is an ocean of choices . We have choices in platform , programming languages ,frameworks etc. There no one to force you what to use and how to use .
The openness and choice always results in innovation . If you look at the enterprises like Google , Facebook ,you will know what type of innovation can happen in open world .
###Mobile is the Future
Mobile devices are in use over decade. But its potential reveled only after iPhone is released . Mobile is the feature . What we do today in the PC , we will be able to do in mobile devices . Mobile devices doesn’t only refers to the smart phones , but they also include netbooks , tablet computers etc . The power of mobile devices growing day by day and its predicted that future generation will doesn’t know what a mouse is !!.
###Can we expect same openness and Choice in future ?
The openness and choice what we enjoying today is for PCs and web. But is same openness and choice will be there in mobile devices . By seeing current scenario I am afraid it will be not.
Apple is the leader in mobile devices . iPhone was named as Jesus phone and AppStore is De facto standard for mobile applications. They have more than 150,000 applications in the store and its a very large compared to second big store ,Android Market, which has only 30,000 apps.
From the above figures its clear that if you want to be developer for the future , you have to develop for the mobile and that too for iPhone . But do you think it will easy?
###Closed platform and Closed minds
Apple is always a closed platform like Windows . But it will create no problem for a developer till they create great applications using the platform . But the iPhone Eco system is closed such that you will start to suffocate in it. The following are the reasons that make you suffocate
-
Develop in their own hardware and OS : To develop for the iPhone you need to own a Mac. Come on man , for developing for a mobile device you have to get a new system altogether? .If you are Mac user then there will be no problem.
-
Closed minds : iPhone SDK policies states that you cannot share what you are making with your fellow. If you do that,then its a offence . What??? is this way you develop applications in the past . We had great communities to help , but now we are helpless.
-
No choice in language and tools : Recent change to iPhone SDK TOS stated that you have to use Apple tools to develop for the iPhone . Which means their own language Objective-C,IDE etc etc. If you are expert in other languages ,you skill sets are waste . You have to learn new language and new tools or stay away.
-
Big boss has to approve your application in order to reach the users : Whenever you developed the apps in the past , there was no one to say “hey let me check the app ,if you cant please me you cant get users” . It was the users who made an app successful or failure . But in the case of iPhone , Apple has to approve the app in order to reach to the user .This means if you are in rival company you cant get your app in Appstore. Google voice is a good example.
Are we going to develop applications like this in feature. Sitting in the dark room, fighting with 80’s language and waiting big boss to approve your app. I fear yes.
###Still hope is there
Though current scenario looks like hopeless , there is a ray of hope in dark called as Android. An open platform which embraces the openness and choices in the Mobile industry . Though its not market leader , it will be in 2014 as projected by IDC.
I am desperate for Android to win, so that i can pursue my dream . There are millions of developer like me who want the same. If it is not going to happen , i will change my field rather than developing for platform like Apple. Whats your stand??


An interceptor that operates pre-save to add audit information to the records being committed that implement the Highway.Data.Interfaces.IAuditableEntity interface
More...
List of all members.
Properties |
| int | Priority [get, set] |
| | The priority order that this interceptor has for ordered execution by the event manager
|
Detailed Description
An interceptor that operates pre-save to add audit information to the records being committed that implement the Highway.Data.Interfaces.IAuditableEntity interface
Constructor & Destructor Documentation
| Highway.Data.Interceptors.AuditableInterceptor.AuditableInterceptor |
( |
IUserNameService |
userNameService, |
|
|
int |
priority = 0 |
|
) |
| |
|
inline |
Creates a interceptor for audit data attachment
- Parameters:
-
| userNameService | Application Service that provides current user name |
| priority | The order in the priority stack that the interceptor should operate on |
Member Function Documentation
Executes the interceptor handle an event based on the event arguments
- Parameters:
-
| context | The data context that raised the event |
| eventArgs | The event arguments that were passed from the context |
- Returns:
- An Interceptor Result
Property Documentation
| int Highway.Data.Interceptors.AuditableInterceptor.Priority |
|
getset |
The documentation for this class was generated from the following file:
- Highway.Data.EntityFramework/Interceptors/AuditableInterceptor.cs


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