Re: [DIYbio] Re: BioCoder : a high-level programming language for expressing biology protocols

Hi BTP Batch2,
I took a look at the BioCoder 1.0 code and got it to compile with make
and gcc on Ubuntu Linux:
https://github.com/nmz787/BioCoder

just make sure you have ncurses-dev installed, something like this:
sudo apt-get install libncurses5-dev libncursesw5-dev

then in the code clone, just run:
make

and the binaries should end up in the Sample_protocol sub-dirs.

Best,
-Nathan

On Mon, Sep 10, 2018 at 10:50 AM, BTP Batch2 <btpb...@gmail.com> wrote:
> Hi Vaishnavi,
> We are students from IIT Roorkee and are currently exploring the domain of
> MicroFluidics. We came across BioCoder and downloaded it from the given
> link.
> So we are facing issues in running the make files. We are working in Linux
> environment. Issues are:
> * cl command not found. (okay, installed cl-launch and then there is no flag
> for -c as present in make file)
> * No such file /FoBioCoder.obj (no of the object files are present.)
> Then we tried using g++/gcc/cc with -c flag and changed *.obj to *.o
> Then conio.h was not found (it was then replaced with curses.h header file)
> using namespace std was also added.
> But finally issue comes in some line where it says.
> ```
> BioCoder.cpp: In function 'void time_constraint(Container&, Time*,
> time_constraint_type)':
> BioCoder.cpp:2818:35: error: invalid operands of types '<unresolved
> overloaded function type>' and 'int' to binary 'operator=='
>    case CURRENT_FLUID: if (time == 0)
>                                    ^
> ```
> We think there is some issue with the maintenance of BioCoder. Can you
> please help us fix that?
>
>
>
> On Tuesday, 8 December 2009 17:56:51 UTC+5:30, Vaishnavi. A wrote:
>>
>> Hi all,
>> I am one of the developers of the BioCoder language. BioCoder is
>> essentially a C library with various functionalities included,
>> pertaining primarily to the field of Molecular Biology. We envision
>> the replacement of natural language description of protocols in
>> published papers with code written in BioCoder, thus making the
>> protocol standardized and amenable to automation and re-usability.We
>> are in the process of working out the release of BioCoder.
>>
>> It is a widely accepted fact that most descriptions of protocols in
>> published papers are ambiguous and incomplete and we are unsure why
>> that is the case. We have come up with a survey to try and understand
>> the problem. It would be great if you could take this short 10-
>> question survey which tries to zero in on the problem. Results will be
>> made available on DIYbio when enough data points have been collected.
>>
>> Please click on the link below to take the survey:
>> http://www.surveymonkey.com/s/SYJM23Q
>>
>> For more information about the language:
>> http://research.microsoft.com/en-us/um/people/thies/thies-iwbda09.pdf
>>
>> To know what BioCoder code looks like, you can check out the following
>> examples from OpenWetWare:
>>
>> http://www.google.co.in/search?q=BioCoder+site%3Aopenwetware.org&ie=utf-8&oe=utf-8&aq=t&client=firefox-a&rlz=1R1WZPB_en-GB___IN356
>
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--
-Nathan