Epilepsy Genomics

DAY 29/08/2024
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1.exploring about epilepsy and seizure

DAY 30/08/2024
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1.exploring about the genomics based epilepsy data
2.finding out dataset

3/9/2024
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1.Exploring the related dataset for epilepsy related to genomics.
2.Exploring about the related gene mutations that can cause epilepsy.

4/9/2024
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1.EXPLORING ABOUT THE GENOMIC BASED STUDY ON EPILEPSY
2.FINDING OUT THE VARIANTS OF GENE CAUSING EPILEPSY IN PATIENTS WITH OTHER DISEASE

5/9/2024
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1.explored the different gene variants in epilepsy.
2.found some de novo mutations resulting in epilepsy.
3.exploring about temporal lobe epilepsy.

6/9/2024
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1.updated the 400 EPOCH TRAINING DATASET OF PATIENTS.

10/9/2024
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1.trained 400 epoch dataset.
2.exploring about genetics of temporal lobe epilepsy.

11/9/2024
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1.tested the 400 epoch dataset
2.exploring the dataset for temporal lobe epilepsy.

12/9/2024
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1.trained the 400 epoch dataset.
2.exploring about the gene databank for epilepsy.

18/9/2024
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1.explored the dataset in gene expression omnibus.
2.identified the different plots in the data representation.
3.identified the comparison between different states in the plots.

19/9/2024
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1.explored the different DATASET FOR TEMPORAL LOBE EPILEPSY
2.ANALYZED THE TOP DIFFERENTIAL EXPRESSED GENES.
3.VISUALISED THE EXPRESSED DATASET USING: VOLACNO PLOT,MEAN DIFFERENCE PLOT,UMAP,VENN DIAGRAM,BOXPLOT,EXPRESSION DENSITY,ADJUSTED P-VALUE HISTOGRAM,MODERATED T-STATISTICS & MEAN VARIANCE TREND.
4.CONVERTED THE R SCRIPT TO PYTHON CODE OF FEW DATASETS.
5.UNDERSTOOD ABOUT THE GEO DATASETS OF NATIONAL LIBRARAY OF MEDICINE.

20/9/2024
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1.EXPLORED THE GENE EXPRESSIONS

23/09/2024
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1.explored about the properties of RNA and DNA.
2.explored the expressed gene variants.

24/9/2024
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1.attended an ISO guidelines class by Mani sir.
2.discussed the explored topics with Dr.Sujatan sir.
3.started to explore the study conducted for epilepsy gene mutations during the time period of 2014-2024.
4.discussed the scope of phenotype data for seizure detection using diagnostic MRI.

25/9/2024
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1.explored the relevant papers for the epilepsy based gene mutations.

26/9/2024
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1.exploring the relevant papers for epilepsy in genomics.
2.understood the wide range of gene mutations in epilepsy by analysing the papers.
3.listing out the specific gene varient for epilepsy.

1/10/2024
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1.exploring papers on genomic study of epilepsy.

7/10/2024
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1.EXPLORING THE PAPAERS BASED ON EPILEPSY.
.

15/10/2024
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1. verified the papers for conference.
2.explored the basics of deep learning .
3.explored the basics of AI and ML.

16/10/2024
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1.verified the mail history of conference.
2.read about the genetics of epilepsy.

18/10/2024
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1.read a paper on genetics of epilepsy.
2.explored the timeline of genetic variations in epilepsy.

21/10/2024
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1.Discuused about the review paper(read) with sujathan sir.
2.Exploring about the AI tools used in epilepsy.

22/10/2024
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1.exploring the AI based genomic data.
2.Explored about any wearable device for epilepsy.

23/10/2024
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1. exploring about the different types of genomic data.
2. explored the genetic variants of genomics.
3. explored the genomic data analysis.
4. exploring about the different parameters used in genomic data

24/10/2024
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1.explored the dataset on openSNP.
2.exploring about the processing of raw data.
3.exploring about different visualisation tools for the explored data.

25/10/2024
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1.extracted the genomic data from FASTQ file and run it in Pycharm.
2.exploring about the epilepsy based genomic data for extraction.
3.exploring about the visualisation tools for ploting the extracted data.

28/10/2024
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1.exploring the dash bio for data visualisation.
2.correcting the error of interpretor.(ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (parmed))
3.installed different packages for dash.

29/10/2024
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1. exploring different visualisation tools for ploting genomic data.
2.exploring different dataset for epilepsy based on genomics.

30/10/2024
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1.explored the librares for mapping data to visual properties(grammar of graphics,Plotline).
2.EXPLORING THE DIFFERENT VISUALISATION TOOLS.

4/11/20224
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1.explored some genomic datasets for epilepsy in animals and humans.

5/11/2024
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1.explored the different gene mutations affected in neurons.
2.explored datset with DNA methyalation(gene mutation) in animals and humans.
3.Attended a meeting with NIMHANS Doctor for the idea of proposal writing and scope of exploration in which field in epilepsy.

6/11/2024
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1. ATTENDED A CLASS ON THE BASICS OF GENOMICS.
2. EXPLORED ABOUT THE DNA REPLICATION AND FORMATION IN CELLS.
3. FORMUALTED AN EXCEL ON BUDGET.

7/11/2024
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1.explored how to download SRA sequencing data from NCBI.
2.explored about SRA toolkit, and how to extract the data from SRA Run selector(fastq-dump SRR955127).
3.explored how to convert the SRA file to FASTQ using some commands (fastq-dump SRR955127.sra)
4.converted SRA file to FASTQ file.

11/11/2024
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1.EXPLORING ABOUT THE DIFFRENT ALIGNMNET TOOLS FOR SEQUENCE DATA IN GENOMICS.
2.FOUND short read aligners s like Bowtie2, BWA-SW, and GSnap.
3.FOUND 2 TYPES OF SEQUENCE ALLIGNMENT:, pairwise sequence alignment (PSA) and multiple sequence alignment (MSA)[PSA considers two sequences at a time whereas MSA aligns multiple
(more than two) related sequences].

13/11/2024
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1.exploring about the area of research in epilepsy with genomic data.
2.exploring about any specific area for research.

18/11/2024
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1.explored about bioinformatics tool for visualizing genomic data.
2.explored the genomic data analysis

20/11/2024
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1.made a workflow for variant analysis.
2.explored the AI based models for genomic research.
3.found some specific gene mutation using AI models in research(KCNQ2).

21/11/2024
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1.exploring the basics of bioinformatics.
2.going through a paper based on history of bioinformatics.

22/11/2024
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1.exploring the bioinformatics in genomics research.

26/11/2024
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1.attended a meeting with NIMHANS team for project discussion.
2.Exploration on FASTQC tool .

27/11/2024
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1.exploring about the FASTQC tool .
2.exploring how to read the analysed data.

28/11/2024
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1. checked the camera ready papers.
2.explored the different parts of fastqc report.

5/12/2024
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1.conference activity-website checking
2.ml testing of patient data
3.exploring about the reserach done on non-communacable diseases in india

6/12/2024
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1.Tested the random forest for upsampled 4096 patient data individualy.

10/12/2024
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1.testing the patient data of 4096 sampling rate with catboost.
2.testing the patient data of 4096 sampling rate with ICA nad PCA added to get better result.

12/12/2024
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1.trained and tested the 4096 sampled patient data with bandpass filter.
2.tested the new data for patient.
3.tested the eventwise patient data.
4.checked the iconbci website and mentioned the corrections.

13/12/2024
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1.TESTED THE NEW EVENT WISE DATA OF 4096 USING CATBOOST.

2/1/2025
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1. Started to write a literature review on AI based genomic analysis for pediatric epilepsy.
2. Explored about the regulatory variant analysis of human cancer.

3/1/2025
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1.Explore how AI applies for regulatory variant analysis of human cancer.
2.Explored the different type of regualatory varaints such as SNVS, large structure genomic data,CNVs.

6/1/2025
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1.Had a meeting with doctors of SCTIMST on 4/1/2025 for AI based genomic analysis for cardiomyopathy and sudden cardiac arrest.
On that basis explored on Genomic analysis for Cardiomyopathy and sudden cardiac arrest .

2.prepared a concept note on Genomic analysis for Cardiomyopathy and sudden cardiac arrest.

7/1/2025
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1.Searched on Pubmed for "Cardiomyopathy in India" and found a paper describing on the recent findings(Dec 2020).
Found around 3623 papers and 58 where selected .

2.while exploring found out that most common reported genes were: MYH7 ,TNNT2,MyBPC3 .

8/1/2025
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1.Explored on epigenetics in cardiomyopathy in India and all around the World.

2. Started to write a literature review on AI based genomic analysis for pediatric epilepsy.

9/1/2025
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1.Explored the different types of omicd data used for varaint analysis.
2.EXplored about the significance of bioinformatics tool for cardiomyopathy patients.
3.Had a meeting with doctors of SCTIMST,on that basis explored how AI model can help to find the genetic cause of some genetic disorders(eg: Long QT SYNDROME)
4.Prepared a concept note on AI based genomic analysis for cradiomyopaathy and sudden cardiac arrest in Kerala,
which says about an AI model that will be helpful for the identification of new varinats from the clinical diagnosis. It helps to identify new varinats and the responsible gene.

10/1/2025
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1.Explored how to build a bioinformatics tool using python.
2.EXplore what are the steps used in bioinformatics
3.EXplored how computaional biology is related to bioinformatics.

1. (self-limited focal epilepsies (SeLFEs))
2. generalized epilepsy syndromes
3. developmental and/or epileptic encephalopathies (DEEs)
   2.Found that recognition of these childhood syndromes requires careful analysis of seizure semiology, evolution over time, and the developmental course of the child, as well as electroencephalographic (EEG) features (background, interictal, and ictal patterns) and, in some cases, brain magnetic resonance imaging (MRI) and genetic studies.
   3.At this time,there are no pathogenic varints arae discovered for any syndromes.

15/1/2025
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1.Explored the omics in healthcare,need for personalised medicine.
2.EXplored about the NGS workflow done in NIMHANS ,how data is preprocessed.
3. Explored the AI driven technologies used for varint interpretation(Alpha Missense, Splice AI) and genomic variant calling (Google Deep Varint ,DRAGEN Bio-IT platform,Sentieon DNAScope machine)

16/1/2025
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1.Attended a meeting with Mani sir for web development on BMI project.
2.Read a paper and found how drug-resistant pediatric treatment is advancing day by day.
some of the specific pediatric epilepsy are Lennox–Gastaut’s syndrome (LGS) and Dravet’s syndrome which have a speciailised drug treatment.

17/1/2025
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1.read a paper on ILAE classification of epilepsy.
2.Prepared a PPT for AI based genomic analysis for pediatric epilepsy
3.attended a class on EEG signal from our team members.

20/1/2025
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1.Read a paper on ILAE classification of epilepsy and found that the epilepsy classification was carried out by a group of team members of task force with expertise in pediatric epilepsy.
They made a draft for each syndrome discussing the mandatory features and exclusionary features for the analysis. They proposed a Delphi method for surveying of all task members in addition to experts in pediatric epilepsy from ILAE regions.
They classified each syndrome with its diagnostic criteria, summary and other features

2.Prepared a PPT for AI based genomic analysis for pediatric epilepsy( corrected previous one).

3.submitted the draft proposal to PI and Co-PI on AI based genomic analysis for pediatric epilepsy.

21/1/2025
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1.learned about the Neural Networks - CNN, architecture of CNN, How CNN is used for data augmentation ,Techniques to improve the CNN performance.

27/1/2025
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1.read a paper for literarture review.
2.collected the details for certificate dispatch(ICON-BCiHT 2024)

28/1/2025
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1.send certificates to the speakers by post(ICON-BCIHT 2024).
2.continuing the literature review.

30/1/2025
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1.Read a paper for literature review.
2.Preparing the body of the literarture review.

31/1/2025
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1.started to write the literature review according to the suggestions.
2.Read papers for literature review

5/2/2025
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1.explored the GATK tool for sequence analysis.
2.Read papers for Literature review.

7/2/2025
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1.Visited GMCT for BMI reading.
2.preparing the literature review

10/2/2025
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1.submitted the literature review , corrections are done according to the suggestions.

13/2/2024
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1.learned about GATK toolkit and prepared a ppt.

17/2/2025
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1.studied the GATK tool.
2.exploring the open access journals for pediatric epilepsy.

18/2/2025
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1.discussed the GATK toolkit with binu sir and mani sir.
2.discussed about the literature review with Dr.sujathan.

19/2/2025
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1. Exploring the different jounals for neurology ,genomics,epilepsy .
2. explored the "Joint variant calling" in GATK .

20/2/2025
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1.EXPLORING ON OTHER SEQUENCING TOOLS such as : BWA, Bowtie etc
2.referred other sites for publishing literature review (google scholar,pubmed).

21/2/2025
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1.exploring on the BWA.
2.searched the GATK python code on github.

24/2/2025
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1.Studied and prepared a ppt for BWA.
2.Studing and Preparing a PPT on Bowtie.

25/2/2025
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1.searched GATK python code, but didn't found it. GATK is written in Java. We can call GATK from python via subprocess.
2.explored the "subprocess" module in python, used to execute system commands and interact with external programs directly from a Python script.
3.We can use "subprocess" module to run BWA commands like indexing, alignment, and sorting.

27/2/2025
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1. Attended a class on "Embedded genomics" by the faculty of IIT Jammu.
2. explored a Python code on snake make-illumina-gatkvariant from GitHub

3/3/2025
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1. Converted the literature review in the template of the EXCIL journal
2. Discussed the SVM with team members.

4/3/2025
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1. Learned about the KNN model generation using scikit-learn.
2. Ran a code for simple linear regression.

5/3/2025
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1.Explained the linear regression to the team members and mani sir.
2. Made a presentation on linear regression and its types.
3. Explained a code for simple linear regression.

6/3/2025
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1.explored a sample gatk python code.
2.explored how regression is used in genomic analysis.

7/3/2025
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1.encountered an error in gatk python code, dealing with the error correction.
2.found new changes in literature review and made corrections.

10/3/2025
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1.attended class on machine learning algorithms and KNN model from team members.
2.searched about genomeindia project and its intiatives for the public.

11/3/2025
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1.read new papers for literature review related to genomic analysis.
2.explored logistic regression

12/3/2025
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1.wrote an intermediate grant propsal
2.Prepared a ppt for logistric regression

14/3/2025
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1.explore CNN
2.explored how DL involves in genomic analysis?

17/3/2025
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1.exploring about LSTM
2.exploring about Multiple layer LLM.

19/3/2025
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1.Explored LSTM and prepared a ppt.
2.executed a python code for LSTM.

20/3/2025
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1.combined the Ml codes in google drive and shared it with Mani sir and Binu sir.
2.prepared a biodata
3.explored multiple layer llm

24/3/2025
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1.explored Deep Learning
2.exploring multiple layer llm.

26/3/2025
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1.prepared resumes
2.explored llm

27/3/2025
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1.attended a meeting with binu sir and byju sir
2.explored a sample fastq file and executed it in python
3.explored a sample csv file for genomics and executed it in python

28/3/2025
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1.Explained the concept of LLM to Mani sir
2.Explored genomic data for genome variant anlysis

1/4/2025
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1.Discussed the concept of using LLM in genomic analysis if following are conditions :
i. if child inherits disease causing gene from single parent (either mother or father) dosnot affect the child
ii. if child inherits from both parents ,which makes the child affected
during exploration and discussion came up with a conclusion that LLM models will be able to do multiple decision making and can give pathogenic or non pathogenic predictions

2/4/2025
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1.explored in detail about LLM for genome analysis for identifying pathogenic gene variant ;identified that
llm with AI will be good for giving best results.
>LLM can retrieve informations from sources like BioGPT,DNABERT ,chatgpt about the genomic text analysis and knowledge retrieval
->AI model will be used for variant analysis and disease risk prediction
--> Hybrid LLM+AI model will be bset for this condition

2.explored TRIO analysis

3/4/2025
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1.Explored about AI-MARRVEL: A Knowledge-Driven AI System for Diagnosing Mendelian Disorders

--> INPUT: uses clinical data,phenotypes(HPO),Sequence(VCF)
--> MODEL: random forest, decision tree
--> Output: able to detect the Pathogenicity scores, Ranked list of variants, Functional annotations, AI-driven disease association predictions.

Inspiration from AIM can help to build an AI model for identifying pathogenic gene variants in pediatric epilepsy.

5/4/2025
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1.Completed the proposal on AI-driven genomic analysis for pediatric epilepsy.
2.Explored the ensemble Machine learning classifier for the detection of pathogenic and non-pathogenic gene variants from the input data(clinical data,phenotypes(HPO),Sequence(VCF))
3.Found that LLM can be involved in the detection of pathogenic gene variant.

7/4/2025
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1.explored the multiple head attention block in Transformer architecture
-->each haed has seperate "scaled dot-product attention" block.
-->each haead its own Qury(Q),Key(K)and Value(V)
--> all heads are concatenated ,once all compuatations are done
-->The concatined output is given to final weight matrix
2. executed a sample python code for Multiple Head Attention block.

15/4/2025
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1.continuing a model creation for llm based genomic analysis.

17/4/2025
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1.Continuing the llm model preparation...
successfully loaded the pre-tarined LLm models.

21/4/2025
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1.continuing the llm model preparation
2.ssvp data collection

22/4/2025
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1.ssvep data recording
2.loading the LLM pretrained models

23/4/2025
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1.Loaded the DNABERT model
2.Fine-tuning the DNABERT model (continuing)
3.preprocessed the input data

24/4/2025
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1.eeg dicom viewer-exploprating
2.DNABERT model (pipeline running)

25/4/2025
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1.submittion of literature review(on process)
2.edf to dicom file convertion(study)

28/4/2025
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1.Prepared a write up for AI based genomic analysis for pediatric epilepsy
2.EDF to DCM file converted

29/5/2025
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1.prepared a technical presentation ppt for national technology day
2.tried to view the dcm eeg file

30/4/2025
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1.prepared for technical presentation.
2.trying to view the converted edf file (dcm file)in a dicom viewer

7/5/2025
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1.correction of review article.
2. individual model preparation and loading(on going)

8/5/2025
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1.loaded individual dnabert model ,correcting the error within the ui.

9/5/2025
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1.correcting the error in loading the model to the ui.
2.tried to view the edf converted dcm file using python code.

13/5/2025
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1.showed the eeg dicom viewer in dash plot

14/5/2025
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1.continuing to convert the eeg dicom viewer in Django
2.completed the correction for literature review

15/5/2025
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1.learned about the basics of web development (overview)
1.learned about the essentials required in web development

16/5/2025
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1.started html tutorial

19/5/2025
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1.completed html
2.complted css

20/5/2025
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1.testing ssvep system
2.testing the ccet system

21/5/2025
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1.tested the ccet device

22/5/2025
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1.tested the ccet device
2.studied the django instalation and creation of new project

26/5/2025
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1.studing the django basics.

27/5/2025
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1.studied the first web app formation.
2.corrected the error's of literature review paper.

29/5/2025
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1.showed the testing of ccet device.
2. continuing the django learning.

3/6/2025
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1.studying the django
2.studying the django-react framework

9/6/2025
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1.Created a sample file upload using node.js
2.learning how to upload a file in django developement server

10/6/2025
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1.Done a file upload in the django development server.
2.Doing the file upload and view for dcm files in the django developement server.

13/6/2025
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1.Completed the file upload and conversion of EDF to DCM file

16/6/2025
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1.Continuing to add the dicom view in django project.

17/6/2025
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1.completed the dicom view for django-react project

18/6/2025
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1.added the metadata in the dicom view.
2.solving the problem with large files convertion and view in dicom.

19/6/2025
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1.Dicom viewer: able to view small file data
Having issues with large files while convertion.

20/6/2025
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1.trying to load large file data using pyedflib and mne
but having issues while converting.

24/6/2025
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1.able to load large file,successfully converted large file data using chunk wise convertion

25/6/2025
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1.Able to view the dicom eeg after convertion.
2.metadata was displayed in the frontend

26/6/2025
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1. Made modifications in the dicom eeg viewer while viewing the waveform
2. modified the frontend for visualisation.

27/6/2025
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1.successfully visualised the dicom eeg waveform after converting it from edf to dcm.
2.A frontend dicom eeg viewer is able to visualise the data with 2sec window size

30/6/2025
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1.Modified the view with scaling , amplitude(mv) according to the original edf file.

9/1/2025
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1. developed standalone application for smriti gmt using pyqt .

16/1/2025
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1. added sound enabled output after each mode completion .
2. modified the output from each mode completion using medals .