gorgitko / molminer

Python library and command-line tool for extracting compounds from scientific literature. Written in Python.

Hello! 👋

My name is Jiri Novotny, I come from the Czech Republic, and I am a bioinformatician.

I am currently working for Immunai as a computational biologist / software engineer.

What do I do in bioinformatics? 🤓

I was doing Ph.D. at the Institute of Molecular Genetics of the Czech Academy of Sciences in the Laboratory of Genomics and Bioinformatics. There I was 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.

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

Now at Immunai I am mostly researching and benchmarking new bioinformatic methods and making sure those we like will land in our internal pipelines (which I also sometimes write from scratch). I am also giving support to our single-cell data curators and of course, fixing bugs (I know, very much unexpected 🙃).

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), 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.

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

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

• See exercise materials for the Analysis of Gene Expression if you want to learn something about the analysis of RNA-seq etc. (these materials are well-suited for self-study)

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.

molminer's Issues

Issue in using molminer

Hey there, When i try to use molminer, i get the following error and Im not sure of it. I have a single pdf file which i wanted to run with ocsr to extract the molecular structure from the pdf.
can some one help me out.

**Cannot perform annotation in ChemSpider: 'chemspider_token' is empty.
Traceback (most recent call last):
File "/home/nx2236/anaconda3/envs/my_new_env/bin/molminer", line 11, in
load_entry_point('MolMiner==1.0.0', 'console_scripts', 'molminer')()
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/cli.py", line 381, in ocsr
result = osra.process(output_formats=["smiles", "inchi", "inchikey"], process_kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/OSRA.py", line 435, in process
stdout, stderr, exit_code = pdf_to_images(input_file, temp_dir, dpi=gm_dpi, trim=gm_trim)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/utils.py", line 257, in pdf_to_images
raise RuntimeError("Error when converting PDF to PNG images. Stderr: {}".format(stderr))
RuntimeError: Error when converting PDF to PNG images. Stderr: /home/nx2236/anaconda3/envs/my_new_env/bin/gm.bin: /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/../libtiff.so.5: no version information available (required by /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/libGraphicsMagick.so.3)
/home/nx2236/anaconda3/envs/my_new_env/bin/gm: line 6: 4341 Illegal instruction (core dumped) LD_LIBRARY_PATH=realpath $DIR/../lib/molminer $DIR/gm.bin ${@:1}

how to manually configure osra_reaction.cpp

Hi gorgitko
how to compile the osra_reaction.cpp manually with out gnu+11 , this cpp shows error when running make in osra installation
I checked the installtion guidelines of yours

• osra_reaction.cpp compile manually without "-std=gnu++11" (see the g++ command which failed and run it manually without "-std=gnu++11")

Issue with OSRA

calling osra through the command line is giving error as:

/minoconda/envs/my_new_env/bin/osra: line 6: 52971 Illegal instruction (core dumped) LD_LIBRARY_PATH=realpath $DIR/../lib/molminer $DIR/osra.bin ${@:1}

Please help.

Simple way of installing dependencies

Hi,

Just want to share with you how to install those cheminformatics dependencies easily with homebrew. see more details on https://github.com/mcs07/homebrew-cheminformatics.

I tried on my MacOS, it works pretty well. Just thought it would be helpful.

LinkError: pre-link script failed for package jirinovo::pubchempy-1.0.3-py_0

Preparing transaction: done
Verifying transaction: done
Executing transaction: failed

LinkError: pre-link script failed for package jirinovo::pubchempy-1.0.3-py_0
location of failed script: /home/pan081/miniconda3/pkgs/pubchempy-1.0.3-py_0/bin/.pubchempy-pre-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: + /miniconda3/envs/my_new_env/bin/python /miniconda3/pkgs/pubchempy-1.0.3-py_0/link.py
/miniconda3/pkgs/pubchempy-1.0.3-py_0/bin/.pubchempy-pre-link.sh: line 2: /miniconda3/envs/my_new_env/bin/python: No such file or directory