fix readme

README.md

@@ -33,3 +33,72 @@ To enroll in this course, students should have completed:
 
 * **One semester of undergraduate biochemistry**
 * **Statistical thermodynamics** (or consent of the instructor)
+
+## Office hours
+ZLS on Monday 5:00 pm CLSL A552, 
+Tianyu Wu on Thursday 4:00 pm-5:00 pm RAL 44
+## Homework due
+Friday nights. 
+
+## Contents
+
+### [Week1](https://forxhunter.github.io/CHEM576/jekyll/2025-01-01-week1.html)
+
+[Week1](https://forxhunter.github.io/CHEM576/jekyll/2025-01-01-week1.html)  Web Resources & Databases for Proteins, Nucleic Acids, Genomes, Subcellular Pathways
+and Networks: Deep Learning Neural Networks (NN), Sequence/Structure Alignment
+Algorithms, Visualization (UNIPROT, SWISSPROT, PDB, SCOP, CATH, NCBI, KEGG,
+YEASTbook, BRENDA: Smith-Waterman, STAMP, VMD/MultiSeq tutorial, Biopython)
+
+### [Week 2](https://forxhunter.github.io/CHEM576/jekyll/2025-01-02-week2.html)
+
+[Week 2](https://forxhunter.github.io/CHEM576/jekyll/2025-01-02-week2.html) : Evolutionary Concepts in Bioinformatics: Comparisons of sequences and structures and
+structure prediction (Phylogenetic Trees, MAFFT, Blast, AlphaFold3, Foldseek)
+
+### [Week 3](https://forxhunter.github.io/CHEM576/jekyll/2025-01-02-week3.html)
+
+[Week 3](./subsections/week3.md): Force Fields for Biomolecules and an Introduction to Molecular Dynamics Simulations
+(Nobel Prize 2013, CHARMM, AMBER, NAMD2, MARTINI/GROMACS)
+
+### [Week 4](./subsections/week4.md)
+
+[Week 4](./subsections/week4.md): Analyzing Molecular Dynamics Simulations: Ligand Binding, Protein Interactions
+( NAMD2 and MARTINI/GROMACS tutorials, radial distribution and correlation functions)
+
+### [Week 5](./subsections/week5.md)
+
+[Week 5](./subsections/week5.md): Simulations of Protein:RNA and Protein:DNA Complexes and their Assembly
+( Ribosome biogenesis, Protein/Nucleic Interactions, Network Analysis,)
+
+### [Week 6](./subsections/week6.md)
+
+[Week 6](./subsections/week6.md): Introduction to Systems Biology and Steady-State Analysis of Metabolic Networks
+(Breuer et al. elife 2019, CobraPy, ESCHER)
+
+### [Week 7](./subsections/week7.md)
+
+[Week 7](./subsections/week7.md): Subcellular Networks for DNA Replication, Transcription, and Translation in a Minimal
+Cell (Stochastic gene expression, Thornburg et al. Cell 2022, Gilbert et al. FCellDevBio 2023)
+
+### [Week 8](./subsections/week8.md)
+
+[Week 8](./subsections/week8.md): Whole Cell Kinetic Modeling and Simulations: Coupled Stochastic Gene Expression and
+Metabolism ( Reaction-Diffusion Master Equation (RDME), Lattice Microbes tutorials, Juypter
+python notebook, machine learning kinetic parameters)
+
+### [Week 9](./subsections/week9.md)
+
+[Week 9](./subsections/week9.md): Atomistic Simulations of a Minimal Cell (NSF STC QCB tutorials MARTINI/GROMACS
+2024)
+
+> Contents provided by Jan Stevens
+
+### [Week 10](./subsections/week10.md)
+
+[Week 10](./subsections/week10.md): Machine Learning of Minimal Cell Trajectories and Selection of Class Computational
+Projects
+
+> Contents supported by Rong Wei in Shulei Wang's group
+
+### Weeks 11-14
+
+Presentations of Computational Projects