gorgitko / microboard-projects Goto Github PK

Some of my microboard projects.

License: MIT License

microboard-projects's Introduction

Hello! 👋

My name is Jiri Novotny, I come from the Czech Republic, and I am a bioinformatician. Currently I am doing a Ph.D. at the Institute of Molecular Genetics of the Czech Academy of Sciences in the Laboratory of Genomics and Bioinformatics.

Recently I have joined Immunai as a single-cell data curator / computational biologist.

What do I do in bioinformatics? 🤓

I am usually analyzing transcriptomic data: bulk and single-cell RNA-seq, and qPCR. But I also have some proficiency in general bioinformatics (all those formats, command line tools, etc.) and other methods, e.g. variant calling, chromatin accessibility (ATAC-seq), TCR sequencing, etc.

I like to help biologists to interpret their data in form of reports and visualizations, as well as public services and databases. I am interested in cancer biology, mainly in the tumor microenvironment, extracellular matrix remodeling, and cancer-associated fibroblasts.

scdrake - a pipeline for droplet-based single-cell RNA-seq data.

What can I do besides bioinformatics? 🤔

I am fluent in R and Python and have experience in making pipelines, general data wrangling and visualization, web development (Python/Django, R/Shiny, HTML5/CSS3, JavaScript), UNIX scripting (bash) and system administration, Git versioning and continuous integration (GitHub Actions). I like to write clean code and documentation (and really appreciate if others also do so 😊). Occasionally, I contribute to open-source projects, or at least open constructive issue tickets.

AmtDB - database of ancient human mitochondrial DNA (private code, full-stack developer role).

I am also teaching practicals in the Analysis of Gene Expression at the University of Chemistry and Technology in Prague.

Exercise materials for the Analysis of Gene Expression

To grab the chance to promote my study programme, here is the link: http://studuj.bioinformatiku.cz/

I would say, it's not an easy, but interesting and satisfying field and the future is bright as more people are needed to analyze the neverending, large bunch of biological data or to develop tools that make this task easier for others.

Several times I was also participating as a lecturer at Prague Autumn School - RNASeq Data Analysis Workshop organized by SeqMe company.

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microboard-projects's Issues

not working with my WeMos D1

to many errors while compiling :(

Arduino: 1.8.13 (Windows 7), Board: "WeMos D1 R2 & mini, 80 MHz, 4M (1M SPIFFS), v2 Prebuilt (MSS=536), Disabled, None, 115200"


In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:34:0,

                 from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:89,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sMethodCore.h:105:17: error: variable or field 'IRAM_ATTR' declared void

     static void IRAM_ATTR i2s_slc_isr(void)

                 ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sMethodCore.h:105:17: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sMethodCore.h:105:43: error: ISO C++ forbids declaration of 'i2s_slc_isr' with no type [-fpermissive]

     static void IRAM_ATTR i2s_slc_isr(void)

                                           ^

In file included from C:\Users\Home64\AppData\Local\Arduino15\packages\esp8266\hardware\esp8266\2.4.0\cores\esp8266/pgmspace.h:10:0,

                 from C:\Users\Home64\AppData\Local\Arduino15\packages\esp8266\hardware\esp8266\2.4.0\cores\esp8266/Arduino.h:241,

                 from sketch\ws2812_controller.ino.cpp:1:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sMethodCore.h: In member function 'void NeoEsp8266I2sMethodCore::InitializeI2s(uint32_t, uint32_t)':

C:\Users\Home64\AppData\Local\Arduino15\packages\esp8266\hardware\esp8266\2.4.0/tools/sdk/include/ets_sys.h:170:54: error: invalid use of member function (did you forget the '()' ?)

     ets_isr_attach(ETS_SLC_INUM, (int_handler_t)(func), (void *)(arg))

                                                      ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sMethodCore.h:269:9: note: in expansion of macro 'ETS_SLC_INTR_ATTACH'

         ETS_SLC_INTR_ATTACH(i2s_slc_isr, NULL);

         ^

In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:89:0,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h: At global scope:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:214:29: error: expected unqualified-id before '[' token

     NeoEsp8266DmaMethodBase([[maybe_unused]] uint8_t pin, uint16_t pixelCount, size_t elementSize, size_t settingsSize) : 

                             ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:214:29: error: expected ')' before '[' token

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:251:10: error: variable or field 'IRAM_ATTR' declared void

     void IRAM_ATTR Update(bool)

          ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:251:10: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:251:31: error: ISO C++ forbids declaration of 'Update' with no type [-fpermissive]

     void IRAM_ATTR Update(bool)

                               ^

In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:90:0,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sDmx512Method.h:161:35: error: expected unqualified-id before '[' token

     NeoEsp8266I2sDmx512MethodBase([[maybe_unused]] uint8_t pin, uint16_t pixelCount, size_t elementSize, size_t settingsSize) : 

                                   ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sDmx512Method.h:161:35: error: expected ')' before '[' token

In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:90:0,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sDmx512Method.h:198:10: error: variable or field 'IRAM_ATTR' declared void

     void IRAM_ATTR Update(bool)

          ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sDmx512Method.h:198:10: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266I2sDmx512Method.h:198:31: error: ISO C++ forbids declaration of 'Update' with no type [-fpermissive]

     void IRAM_ATTR Update(bool)

                               ^

In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:91:0,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:40:27: error: 'IRAM_ATTR' declared as an 'inline' field

     static inline uint8_t IRAM_ATTR GetTxFifoLength(uint8_t uartNum)

                           ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:40:27: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:40:68: error: ISO C++ forbids declaration of 'GetTxFifoLength' with no type [-fpermissive]

     static inline uint8_t IRAM_ATTR GetTxFifoLength(uint8_t uartNum)

                                                                    ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:45:24: error: variable or field 'IRAM_ATTR' declared void

     static inline void IRAM_ATTR Enqueue(uint8_t uartNum, uint8_t value)

                        ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:45:24: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:45:72: error: ISO C++ forbids declaration of 'Enqueue' with no type [-fpermissive]

     static inline void IRAM_ATTR Enqueue(uint8_t uartNum, uint8_t value)

                                                                        ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:50:36: error: expected ';' at end of member declaration

     static const volatile uint8_t* IRAM_ATTR FillUartFifo(uint8_t uartNum,

                                    ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:50:36: error: redeclaration of 'const volatile uint8_t* NeoEsp8266UartContext::IRAM_ATTR'

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:40:27: note: previous declaration 'uint8_t NeoEsp8266UartContext::IRAM_ATTR'

     static inline uint8_t IRAM_ATTR GetTxFifoLength(uint8_t uartNum)

                           ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:52:36: error: ISO C++ forbids declaration of 'FillUartFifo' with no type [-fpermissive]

         const volatile uint8_t* end);

                                    ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:82:17: error: variable or field 'IRAM_ATTR' declared void

     static void IRAM_ATTR Isr(void* param, void* exceptionFrame);

                 ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:82:17: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:82:64: error: ISO C++ forbids declaration of 'Isr' with no type [-fpermissive]

     static void IRAM_ATTR Isr(void* param, void* exceptionFrame);

                                                                ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:244:10: error: variable or field 'IRAM_ATTR' declared void

     void IRAM_ATTR InitializeUart(uint32_t uartBaud, bool invert)

          ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:244:10: error: expected ';' at end of member declaration

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266UartMethod.h:244:65: error: ISO C++ forbids declaration of 'InitializeUart' with no type [-fpermissive]

     void IRAM_ATTR InitializeUart(uint32_t uartBaud, bool invert)

                                                                 ^

In file included from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:0:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h: In instantiation of 'NeoPixelBus<T_COLOR_FEATURE, T_METHOD>::NeoPixelBus(uint16_t, uint8_t) [with T_COLOR_FEATURE = NeoGrbFeature; T_METHOD = NeoEsp8266DmaMethodBase<NeoEsp8266DmaSpeedWs2812x>; uint16_t = short unsigned int; uint8_t = unsigned char]':

C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:42:73:   required from here

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:128:92: error: no matching function for call to 'NeoEsp8266DmaMethodBase<NeoEsp8266DmaSpeedWs2812x>::NeoEsp8266DmaMethodBase(uint8_t&, uint16_t&, const size_t&, const size_t&)'

         _method(pin, countPixels, T_COLOR_FEATURE::PixelSize, T_COLOR_FEATURE::SettingsSize)

                                                                                            ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:128:92: note: candidates are:

In file included from C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/NeoPixelBus.h:89:0,

                 from C:\Users\Home64\Documents\Arduino\ws2812_controller\ws2812_controller.ino:6:

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:193:5: note: NeoEsp8266DmaMethodBase<T_SPEED>::NeoEsp8266DmaMethodBase(uint16_t, size_t, size_t) [with T_SPEED = NeoEsp8266DmaSpeedWs2812x; uint16_t = short unsigned int; size_t = unsigned int]

     NeoEsp8266DmaMethodBase(uint16_t pixelCount, size_t elementSize, size_t settingsSize) :

     ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:193:5: note:   candidate expects 3 arguments, 4 provided

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:188:34: note: constexpr NeoEsp8266DmaMethodBase<NeoEsp8266DmaSpeedWs2812x>::NeoEsp8266DmaMethodBase(const NeoEsp8266DmaMethodBase<NeoEsp8266DmaSpeedWs2812x>&)

 template<typename T_SPEED> class NeoEsp8266DmaMethodBase : NeoEsp8266I2sMethodCore

                                  ^

C:\Users\Home64\Documents\Arduino\libraries\NeoPixelBus_by_Makuna\src/internal/NeoEsp8266DmaMethod.h:188:34: note:   candidate expects 1 argument, 4 provided

exit status 1

Fehler beim Kompilieren für das Board WeMos D1 R2 & mini.

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