GitHub - gggdttt/BioGo: BioGo is a new programming language developed to operate DMF platform

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In our research group, we currently work on the software, firmware, and hardware development related to digital microfluidic biochips.

Digital microfluidic biochips allow the execution of biological and chemical protocols on a chip-scaled device delivering cost and performance advantages over the traditional benchtop wet lab processes. Building reconfigurable and programmable digital biochips that can be used for a broad range of laboratory protocols inevitably shows the need for an easy and structured process to capture a protocol and translate it into a sequence of steps that can be run on a DMF biochip. This process can be captured with the classical software tool-chain consisting of a programming language, a compiler, and an execution platform. This project aims at defining a domain-specific language to capture biochemical protocols and to develop the necessary front-end compilation tools for such a language. Besides capturing the biochemical protocol, the language should allow the programmer to define behavior when special conditions arise due to droplet missed-movements events and other phenomena that may disrupt the protocol's normal execution.

If time allows, the project may also include the development and implementation of back-end techniques for scheduling and routing of droplets and generation of low-level commands.

Design

Our project's basic structure looks like:

DESIGN->WRITE CDMF-> COMPILE TO C# CODE -> FIND PATH -> GENERATING INSTRUCT FOR CHIP

|=====User=========|=======Compiler======|=============Executor======================|

Compiler

Syntax

Declaration

droplet <name>;
// 		string

Input

input(<droplet_name>, x,y, size);
//      string, int, int, float

Move

move(<droplet_name>, x_dest, y_dest);
//		string, int ,int

Merge

merge(<out_dest_droplet_name>,<in_1_droplet_name>,<in_2_droplet_name>,x_dest,y_dest);
// 		string, string, string, int, int

Split

split(<out_dest_name1>,<out_dest_name2>,<in_droplet_name>,left_x_dest, left_y_dest, right_x_dest, right_y_dest, ratio);
// string, string, strig, int, int ,int, int, real
// note: ratio is D1/(D1+D2)

Mix

mix(<droplet_name>,x_mix,y_mix,size_x,size_y,repeat_times)
// 	string, int ,int ,int ,int int

Output

output(<droplet_name>, x, y)
// string, int ,int

Store

store(<droplet_name>,x,y, time)
// string, int, int , float

*Repeat

repeat <N> times{ <operation1>; <operation2>; ... <operation_N>;}
// example:
repeat 10 times{
move(d1,3,3);
move(d2,7,7);
move(d1,5,5);
move(d2,10,10);
}

Input and Output

Input : Source code of sc file.

Output: JSON format

Input example:

# this is a demo

# droplet declaration
droplet d1;
droplet d2;
droplet d3;

# droplet input
input(d1,1,1,1.0);
input(d2,4,4,0.5);
input(d3,10,10,3.2);

# move
move(d1,3,3);
move(d2,7,7);
move(d3,9,9);

# split 
# d3-> d4, d5
droplet d4;
droplet d5;
split(d4,d5,d3,12,12,15,15,0.5);

# merging
# d4,d5->d3
merge(d3,d4,d5,5,9);

# mixing
mix(d3,2,2,2,2,5);

# store
store(d3,5,5,2.0);

# output
output(d1,0,0);
output(d2,0,0);
output(d3,0,0);

output example:

[
  {
    "$type": "Executor.Model.Operation.DropletDeclarator, Executor",
    "name": "d1",
    "line": 4
  },
  {
    "$type": "Executor.Model.Operation.DropletDeclarator, Executor",
    "name": "d2",
    "line": 5
  },
  {
    "$type": "Executor.Model.Operation.DropletDeclarator, Executor",
    "name": "d3",
    "line": 6
  },
  {
    "$type": "Executor.Model.Operation.DropletInputer, Executor",
    "line": 9,
    "name": "d1",
    "xValue": 1,
    "yValue": 1,
    "size": 1.0
  },
  {
    "$type": "Executor.Model.Operation.DropletInputer, Executor",
    "line": 10,
    "name": "d2",
    "xValue": 4,
    "yValue": 4,
    "size": 0.5
  },
  {
    "$type": "Executor.Model.Operation.DropletInputer, Executor",
    "line": 11,
    "name": "d3",
    "xValue": 10,
    "yValue": 10,
    "size": 3.2
  },
  {
    "$type": "Executor.Model.Operation.DropletMover, Executor",
    "line": 14,
    "name": "d1",
    "xDest": 3,
    "yDest": 3
  },
  {
    "$type": "Executor.Model.Operation.DropletMover, Executor",
    "line": 15,
    "name": "d2",
    "xDest": 7,
    "yDest": 7
  },
  {
    "$type": "Executor.Model.Operation.DropletMover, Executor",
    "line": 16,
    "name": "d3",
    "xDest": 9,
    "yDest": 9
  },
  {
    "$type": "Executor.Model.Operation.DropletDeclarator, Executor",
    "name": "d4",
    "line": 20
  },
  {
    "$type": "Executor.Model.Operation.DropletDeclarator, Executor",
    "name": "d5",
    "line": 21
  },
  {
    "$type": "Executor.Model.Operation.DropletSplitter, Executor",
    "line": 22,
    "outDestName1": "d4",
    "outDestName2": "d5",
    "inDropletName": "d3",
    "outDest1X": 12,
    "outDest1Y": 12,
    "outDest2X": 15,
    "outDest2Y": 15,
    "ratio": 0.5,
    "_order_id": 0
  },
  {
    "$type": "Executor.Model.Operation.DropletMerger, Executor",
    "line": 26,
    "outDropletName": "d3",
    "inDroplet1Name": "d4",
    "inDroplet2Name": "d5",
    "xDest": 5,
    "yDest": 9
  },
  {
    "$type": "Executor.Model.Operation.DropletMixer, Executor",
    "line": 29,
    "name": "d3",
    "xMix": 2,
    "yMix": 2,
    "xDistance": 2,
    "yDistance": 2,
    "repeatTimes": 5
  },
  {
    "$type": "Executor.Model.Operation.DropletStorer, Executor",
    "line": 32,
    "name": "d3",
    "xValue": 5,
    "yValue": 5,
    "latency": 2.0,
    "time": 0
  },
  {
    "$type": "Executor.Model.Operation.DropletOutputer, Executor",
    "line": 35,
    "name": "d1",
    "xValue": 0,
    "yValue": 0
  },
  {
    "$type": "Executor.Model.Operation.DropletOutputer, Executor",
    "line": 36,
    "name": "d2",
    "xValue": 0,
    "yValue": 0
  },
  {
    "$type": "Executor.Model.Operation.DropletOutputer, Executor",
    "line": 37,
    "name": "d3",
    "xValue": 0,
    "yValue": 0
  }
]

Exception Diagnostics

Exceptions of Compiler

1.'{0}' is not declared

Exception message: C_DROPLET_NOT_DECLARED

Exception code: 00001

Code example1:

# the beginning of file
droplet d1;
droplet d2;

input(d3,10,10,3.2);

Code example2:

# the beginning of file
input(d1000,10,10,3.2);

2.'{0}' is declared more than once

Exception message: C_DROPLET_DECLRATED_MORE_THAN_ONCE

Exception code: 00002

Code example:

droplet d1;
droplet d1;

3.Incorrect syntax

Exception message: C_INCORRECT_SYNTAX

Exception code: 00003

Code example1:

droplet; d1#
inputtt();

4. Occupied variable has not been released

Exception message: C_VARIABLE_NOT_RELEASED

Exception code: 00004

Code example:

droplet d1;
input(d1,3,3,3);
input(d1,3,3,3);

5. Variable does not assign a value

Exception message: C_VARIABLE_NOT_ASSIGN_VALUE

Exception code: 00005

Code example:

droplet d1;
move(d1,3,3);

Exceptions of Executer

1. Illegal position value

Exception message: E_ILLEGAL_POSITION

Exception code: 00001

Code example1:

#in config.xml, the chip is 32x20
droplet d1;
input(d1, 33, 10, 0.05) # x value bigger than chip's width
input(d1, -1, 10, 0.05) # x value smaller than 0
input(d1, 10, 21, 0.05) # y value bigger than chip's width
input(d1, 10, -1, 0.05) # y value smaller than 0

2.Illegal droplet's size value

Exception message: E_ILLEGAL_DROPLET_SIZE

Exception code: 00002

Code example:

input(d1, 1, 1, 5.0) # Here the droplet is 3ml, the chip can not contain such size droplet

3.

Exception message: C_DROPLET_DECLRATED_MORE_THAN_ONCE

Exception code: 00002

Code example:

4.

Exception message: C_DROPLET_DECLRATED_MORE_THAN_ONCE

Exception code: 00002

Code example:

5.

Exception message: C_DROPLET_DECLRATED_MORE_THAN_ONCE

Exception code: 00002

Code example:

6.

Exception message: C_DROPLET_DECLRATED_MORE_THAN_ONCE

Exception code: 00002

Code example:

Exception/Errors

The exception is not throwed by compiler, it is throwed by executor

Error001: droplet out of bound
Error002: can not split droplet for there is not enough space
Error003: can not mix droplet for there is not enough space (maybe merged with error02)
Error004 : can not find a route

Rules check

By compiler

Invalid 1: droplet is not defined before
Invalid 2: position is out of bound (should this be handled as exception?)

Path-finding algorithm

Now only Astar and Simple XY supported.

Conflict-based searching?

AStar

For example, there is a red droplet (2x2) wants to move to the white space.

Our astar router will use its left-top position as the moving element. And at the same time, all other droplets (and the right-bottom bounds) will be reckoned as block elements.

Assume there is a red droplet(3x3) wants to move to the white space:

The moving element is shown in the following image:

Name		Name	Last commit message	Last commit date
Latest commit History 95 Commits
ANTLRSupporter		ANTLRSupporter
BioCompiler		BioCompiler
Executor		Executor
MicrofluidSimulator		MicrofluidSimulator
Tool		Tool
out		out
test		test
.gitignore		.gitignore
Config.xml		Config.xml
MicrofluidCompiler.sln		MicrofluidCompiler.sln
MicrofluidCompiler.sln.licenseheader		MicrofluidCompiler.sln.licenseheader
MicrofluidSimulator.sln.licenseheader		MicrofluidSimulator.sln.licenseheader
README.md		README.md
schedule2.xlsx		schedule2.xlsx
template.basm		template.basm
template.json		template.json

gggdttt/BioGo

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Preview

Design

Compiler

Syntax

Declaration

Input

Move

Merge

Split

Mix

Output

Store

*Repeat

Input and Output

Input example:

output example:

Exception Diagnostics

Exceptions of Compiler

1.'{0}' is not declared

2.'{0}' is declared more than once

3.Incorrect syntax

4. Occupied variable has not been released

5. Variable does not assign a value

Exceptions of Executer

1. Illegal position value

2.Illegal droplet's size value

3.

4.

5.

6.

Exception/Errors

Rules check

Path-finding algorithm

AStar

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